Welllll, I read through most of it and wrote down my stronger thoughts. I'm not sure how things fall on the balance side, since I haven't played it, but some things threw up red flags. So yeah. Here's the whole text dump:
Poison ninjas focus on damage, and shuriken ninjas on status? Seems counterintuitive at first.
Manaphy and Phione were not created in the modern era (perhaps discovered)
Why is your pokemon system not suited to all pokemon? You should come up with sample mechanics for the pokemon that you decided not to include.
Lots of "see page #" without an actual number (first two paragraphs of page 11, 2nd paragraph of page 13, Pokemon Training Advice Chart)
Why are pokemon with more than one type less likely to paralyze?
Magic bounce is worded very confusingly
Why does water qualify for solid? Isn't it a liquid?
Can wonder skin ever activate?
Why so restrictive with move requirements? Bounce would make sense for spoink, but not as much for Snubbul or Teddiursa. Ghost and psychic types would be more likely to know small quantities of magic than furret or something. Innocence seems like it interferes with roleplaying and isn't really worth taking.
How many blocks of ice can be made with Ice Beam in one turn?
Superheat "anyone touching it takes damage... and depending on the thickness of the object may be malleable" this grammar implies that the people will be malleable depening on the thickness of the object. Doesn't make sense.
Green thumb - does not specify how long pokemon must sleep for (a half hour? one round of combat?)
Striding pads would be cooler if they worked in battle.
Wither - "It chooses when to and when to use this." do you mean "when not to"?
Snatch - change "they" to "the victim" for clarity.
Thought Place -"After a minute of preparation which no one may detect this pokemon" means what?
Fissure - Why are you mixing meters and feet? This is just confusing for EVERYONE.
Moving on to classes:
Not having looked at the charts, Yumi seems instantly more flexible than Katana.
Do trainers max at level 10? Seems like a low cap. This means that trainer levels wil probably be harder to get, and players don't get fun new stuff as often.
Majesty sounds like an easy out to not have to roleplay. So does Honor Guilt.
Humble Life - regularity -> regularly
Channeling does not specify what sort of pokemon you can choose (can you choose Ferrothorn, or must you choose one of the legendaries you revere?) Dialga is obviously the best choice from a mechanical standpoint (both dragon and steel are good defensive types).
Purify seems like another roleplaying shortcut. Perhaps instead give a bonus to calming pokemon through talking to them.
Philosophic Mastery seems like a weird move, since philosophy is so much up to personal interpretation. Knowing every possible philosophy behind every possible action of every possible character all at the same time seems a bit overwhelming and impractical.
Controlled breathing seems pretty niche. I can see Kitchen Master getting more use than any of these.
Do pokemon need to eat? How long does Kitchen Master food last?
For Aura Fist, must you always add half of your remaining guard, or can you add less? Please clarify.
"You can create a special shrine in a beuatiful area which no one would normally be able to make with a check." What? Do you have to make a check to make the shrine? How much time does this take? Are you implying that only this PC has the skills to make this sort of shrine? A team of 10 men couldn't do the same? Also, beautiful is misspelled. "Pokemon will out of respect for the gods and pious people will refuse to attack you." Just change to, "Pokemon and pious people will, out of repsect for the gods, refuse to attack you."
Perfect Balance - Can they balance on top of a sewing needle? Why is this Buddhist only?
General question - Can you take a move from a lower level when leveling up, or must you always choose from the options available in that level?
Why does performer only get a whip? Why not a baton?
Naturalist - Sandstorm is actually a rock type move, not steel type. Though steel is the best defensive typing of the three, rock is possibly the best offensive type. Making this choice for the player determines what fighting style they will be better at (at least in sand). Maybe you should let them choose?
Coach - What happens if you write two actions for your pokemon, but your human is knocked out before it can use coach?
Routine - It is spelled "performing" not "preforming," unless you mean "to form beforehand." This spelling mistake appears in every performing-related move.
Storm guide- Change to "Weather never slows down you or..."
Attention Grabber - "you can stop someone from looking for sneaking or hiding people for three minutes." What? I think you mean, "you can stop someone from looking for, sneaking, or hiding people for three minutes." So if there is a guard actively searching for an intruder, you have a free pass to stop them for three minutes? That seems a bit counterintuitive. You can also stop a particular person from sneaking around? That's ok, but they will just start sneaking again after the three minutes are up. Stopping someone else from hiding a person just by grabbing their attention also doesn't make sense, as they could be hiding a person in their cupboard, and are probably not hiding them under a coat or something. It would make more sense if you drew attention from all NPC's within a certain radius for that time, giving them penalties to checks to notice anything else (eg. pickpockets).
Trick - I think you mean "consent" instead of "ascent". Also, this move is basically useless.
Slip - This is even more useful than Samurai's equivalent feature (which is granted much earlier, but still). The combination of the two means that the PC's will probably never have to account for their actions, except through death.
Terrain Maneuvering - Combined with the steel defensive typing from naturalist in a sandstorm, you've suddenly got a whoooooole lot of immunities.
Geographic Knowledge - "You know where everything is." Woah woah, that's a pretty steep buff. Let's see... Where are the bandits that robbed us? Where is their hideout? Where does every merchant household in every town keep their gold? Where does the emperor keep his gold? Where are the easiest, and most exploitable routes to get to these gold stores? Where do the gods live? Where do the gods keep their eggs? Where does our enemy live? Where do his wife and children live? This has the potential to completely take a lot of the mystery out of many campaigns. :/
The last sentence is redundant, because since you know where EVERYTHING is, you of course must always know where you are, and also where all of your party members are, regardless of whether they've been kidnapped or not.
Mutual Understanding - You may want to change Japanese to "your language". I know the game is supposed to take place in Japan, but the book is written in English, and most players will probably be speaking in English, so I could see a mean GM saying, "Well, you don't understand Japanese, but that's what it sounds like the pokemon is speaking." Also, some people may want to take your system and run it in a slightly different setting (eg. a desert) and a different language may be spoken in that setting.
Excuses - Another roleplaying shortcut move. People won't always have a reason good enough to not be arrested (in fact, they will very rarely, if ever, have a good enough reason). A bonus to lending credence to your excuse, and/or bribing the guards would probably be more appropriate.
Perfect Relation - Sort of like mind control here, I'm not sure if this really makes sense. A bonus to spreading rumors might be more appropriate, with more work required to actually convince the person that it happened to them.
Poison pool - Poison chance and Priority from the same move may be a bit much, not sure.
Aim Pool - More versatile than poison pool. Seems like the choice is between being good at poisoning, or being good at every other status.
Violent intent - Seems like auto-intimidation with a downside that it can easily get you into trouble that you don't want. There seems to be a disconnect here, where the character could be saying, "Hey, let's not get in a fight folks, let's all stay calm, I'm sure we can work something out" and the NPC's would automatically think that the ninja is going to start a fight. Probably not worth taking.
Why can only the shuriken mastery ninjas disguise themselves with Peasant Alibi?
Nimble Strike - Looks like the performer version is significantly stronger, which doesn't seem to make sense fluff-wise.
Merchant - How much do throwing bombs and arquebus ammunition cost? What is the difference between them?
Deal - You should maybe give this status condition a name
Downplay - Another roleplaying shortcut feature. Bleh.
Managerial Communication - See Mutual Understanding
Market Espionage - Not as bad as a lot of the others, but still seems like a shortcut instead of good roleplaying.
Anticipatory Ducking - Ranged attacks have a half chance of hitting you? Sounds broken. It's certainly more useful than most features from other classes.
Common Ruler - Should be left to roleplaying. You could possibly give them a bonus to causing a revolt, but this really seems unnecessary.
Asleep - Do you round up, down, or some other way?
Expert Lore makes Managerial Communication and Mutual Understanding redundant.
Searching for an ancient relic - Cool idea, but Geographic Knowledge makes it almost completely pointless.
Pilgrimage - The last complication will probably not work or be relevant at all if there is a samurai or performer in the party.
Hidden Power would make more sense as Secret Power if you follow the main series games.
Getting to the more general now that I've read most of it, I somewhat like how general and customizable the pokemon are. On the one hand, this makes all pokemon of the same type basically the same, but on the other hand this allows players to use the pokemon that they like without penalty. What I don't really like is that human characters are very restricted in what they can learn in their class; I guess this is just a personal thing, but I like to have more freedom in character creation. On the one hand, the simplicity of the system makes it accessible, but on the other hand it has the potential to remove a lot of that delicious strategy from the game. For example, I was pretty disappointed to find that Teeter Dance was changed to a 1-target move. But I think there's a different sort of strategy here that I'd really need to play it to see.
I like that you provide a lot of help for new players and new GM's. While the system would likely be good for new players, the flaws (eg. the ability for PC's to sway NPC's and escape imprisonment without contest, and Geographic Knowledge) make this an extremely treacherous system for new GM's. The problem with these sorts of features is that it takes the power out of the GM's hands, and puts it in the player's hands. If a GM decides that a certain field move doesn't work this time (even though the field move says that it always works), the player will feel cheated, while if the GM allows it, their story may be ruined. Building the potential for that sort of incident into the system is generally a bad idea.
In addition to fixing these, I'd like it if you could provide some sample items and how much they would cost, in gold and/or in rice, especially rations. Yes, it's ultimately up to the GM, but having some base numbers to work with really helps new GM's, and they can always adjust things on the fly. Plus, if there is nothing to buy, why would the PC's care about getting robbed by bandits, acquiring fame and fortune, or any stash of treasure? Why would a merchant class even matter in a game where there's nothing to buy or sell but rice? There also isn't a way for players to get more pokemon, and while that could be left up to roleplaying and letting the players seek out what they want, leaving all pokemon-aquisition up to that seems strange when you put in so many player abilities to let them do things without needing to roleplay.
Part of me wants to run it RAW just to see how much of a trainwreck it would be. But I have too much else to do. I think this system has potential, but for me personally it would take too much effort to fill in all of the blanks to make a deep and interesting campaign.
That is quite the list. Thank you very much for bringing it to my attention! Editing issues asside (which were surprisingly numerous, but admittedly I did rush the production a lot), your criticisms about the scope of lots of the powers and things like the shuriken vs poison strangeness were very poignant. Rather than edit the original book, because I have many very fundamental problems with the way the game is designed now, I'm going to be releasing a second edition some time this year that is going to fundamentally alter almost everything about the game.
Right now I am working on a couple of different projects. I've released an unrelated tabletop system called Casters & Conquest and am working on another called Amalgama. But after those are done with I'm going to be working the second edition of Pokemon Conquest.