I have very mixed feelings about this game. I definitely like it more than I thought it would, however with its good points there are also some notably bad points. Beware, there are spoilers ahead.
I'll start with the good points.
-Firstly, I haven't noticed any spelling or grammar errors yet (although there may have been some minor ones that I didn't remember). This makes the game seem a lot more professional and well-done.
-The setting is really unique. It defines the look and feel of your game, and makes it interesting. I love finding the little nooks and crannies in the world.
-The "scarcity" of pokemon also presents a unique challenge, providing good motivation for sidequests, and making the discovery of even less-popular pokemon exciting.
-There are actual characters, and they actually have personalities. The story is also interesting, I have bits and pieces but can't put the whole picture together yet (whereas in official pokemon games, everything is usually more-or-less clear).
-Dream world abilities have been present where they're awesome (eg. Contrary Snivy, Technician Meowth) but I've been able to find pokemon without them where I want to (eg. Ekans)
-This game was obviously made by someone with at least some competetive battling experience, judging from the books in the trainer's school, and the gym leaders' rosters. The gym leaders are challenging not (just) because they are higher-leveled than you, but also because of the variety of types and their movesets.
-While some sprites are very clearly edited, and some look a little hacked together, for the most part the graphics look fine and don't detract from the experience.
-The music is usually pretty fitting. I especially love the rival battle theme.
-I felt that the park sequence was very well done, seeing the other characters tied up by vines as I walked by was pretty eerie. Also, the machine with the tangrowth as a plot point is not something I've ever seen in a pokemon game, but it still felt like it fit in with the world while still being different.
Now for the bad:
-The first and second gym leaders have six pokemon? The first one wasn't bad because I swept through about half of them with my Spinda, but I was honestly quite surprised, and a little jarred. A warning might be nice.
-I found a teddiursa, but I couldn't figure out where it ran off to. If you expect your players to ever find it, you might want to give them a hint, or have it hide nearby. Unless it's important to the story later or something.
-This game is pretty difficult, which is fine. The problem is that you don't balance it so that the players can deal with that difficulty. I am stuck at the second gym and here are the problems I'm having:
-The shops don't sell you more items as you get more badges, like in the real games. The gym leaders use several Super Potions, which I don't even have the opportunity to buy. This is not much of a problem in the first gym, since super potions are almost more than you need at that point, but going against the second gym without them is ridiculous. As a player, I feel cheated that the computer players have more tools at their disposal than I will have the opportunity to have.
-I have beaten all of the available trainers, but my pokemon still aren't strong enough to beat the gym. I don't have access to any useful TM's, and have no idea how to get Heart Scales, so I can't adjust my pokemon's movesets to better fit the problem. This leaves me with two options, 1. Train up a fire or fighting type pokemon to try to help. I don't like this option because it feels like I'm being bullied into using certain pokemon, but it's what I'll probably do. 2. Grind my existing team up a few levels in hopes that I'll stand a better chance. Having the only options be "grinding, or more grinding" are already annoying, and a sign of bad game design. Also, since I've beaten all of the trainers, and there is no rebattling (not your fault, I suppose), I would be forced to grind on pokemon around level 14, over 10 levels lower than my current team. It honestly takes more time than it is probably worth (especially since every place with wild pokemon is pretty far from the pokemon centers).
So, basically, a summary of the problem is this:
1. You can make your team out of any of X pokemon available (pretty standard)
2. Unless you build your team X way, using the tools you don't have (or using the pokemon that the gym guy tells you to use) you can't beat the gym leaders and advance in the game.
In other words, you're telling the players, "Every choice works, except some choices are wrong." That's pretty bad.
The solution is simple: give your players more options. I don't see why Super Potions aren't available, or why the Silph Dept. Store requires "stickers" to get to higher levels. It's an interesting idea, but it doesn't make much sense in a worldbuilding sense; wouldn't Silph want all people to have access to their products, so they can get more money? If you are worried that the items in the Dept. Store would make the game too easy, just make them a little expensive, so that if the player REALLY wants to put Fire Blast on their Quilava early in the game, they can still do so, they just won't have much money left to buy anything else. That's just my suggestion, anyway.
-While we're on items, Sitrus berries are annoyingly expensive. I suppose it fits the flavor of the world, since they are probably imported, but when they are the only alternative to potions, and are not equal to super potions in power for quite a while, the price seems a bit excessive. It's a little bit of a conflict between flavor and balance here.
-I don't know how I feel about the characters. Many of them very clearly feel like characters instead of people. Julia and "Flobot" in particular have quirks that are a little too over-the-top for them to seem real at all, (though maybe I think this because they annoy me). This contrasts a lot with the inconsequential NPC's littering the city, who for the most part are pretty believable. Like I said earlier, you still gave it a better shot than most pokemon games do.
-Some of the mapping could use a little work. While the overworld city is fine, the factory feels like a series of hallways to get the player to fight the meteor grunts, so they can go find the door, then more hallways so they can find the bombs, so they can get into the final important-looking room and advance the story. It feels very contrived, and doesn't feel like you're in a factory at all. The slums is a bit better, but still suffers from the same problem. Even if your players only visit a place once, if you care about every place you make, your game will have real quality.
-I was ok with the level 17 electrode, but a level 27 Cradily? I know for a fact that it doesn't evolve until level 40. Yes, Ghestis has a Hydreigon that is about 12 levels too low to exist, but there is only one, and *everyone* complains about it. It's not that big of a deal, but it could put people off (especially with the whole gym leaders having more tools thing). (Also, by the time in the game that you fought Ghestis, you effectively had as many full restores and max revies as you wanted.)
-While the Pokemon Gang was completely unexpected, and I thought it was a really cool idea, I was pretty disappointed that I didn't have any opportunity to catch Scraggy or Scrafty afterwards. It was probably mostly because of the big lead-up to the battle, where I had been certain that I was going to be able to catch it once I chased it down. Oh well. I think the idea of the Pokemon Gang attacking you one at a time is unrealistic, though. It may have worked better as a double or (if you have the capability for it) triple battle. (EDIT: After going back I did find and catch one, although I have no idea how I was supposed to know to look there because there were no hints or anything that Scraggy would be there.)
-The game corner prizes are... pretty lackluster. Chingling is pretty weak, and I doubt many people would be willing to work that hard to get their hands on one unless they are trying to complete the pokedex. Shinx, while popular, is not game-breakingly strong, and doesn't become remotely useful until it evolves (and therefore is also probably not worth the effort). I don't even remember what the second choice was. It may be a good idea to change which pokemon are game corner prizes; usually, strong, rare, or hard-to-catch pokemon are game corner prizes (eg. Dratini, Abra, Porygon... this is why I was so happy when I found Porygon in the wild). If the players are gonna work that hard for something, it better darn well be good. Also, it would be nice if there were some good items or TM's for prizes, in case the pokemon aren't motivation enough for the player to play in the game corner.
-There's a really large volume difference in the music... If I turn up the volume to hear the Pokemon Center music, then go outside, I have to turn the volume down. If I get into a battle, I have to turn it way down to prevent damage to my eardrums...
(Here's where I transition more to tips or something)
-Do all of the starters get their dream world abilities? While this is pretty cool, it could definitely cause some balance issues... the game may be significantly harder for someone who picked Chlorophyll Bulbasaur than someone who picked Speed Boost Blaziken. Just something to keep in mind.
-I think it might make the game more believable if Amethyst's exact job, position, rank, or whatever is made known. Her saying, "I'm not a professor, but I do important stuff like one!" made me think your entire game was a complete joke at first. Is she the mayor? Police chief? Author self-insert? The fact that everyone reports things to her when she doesn't seem to have a job other than signing people up for the Pokemon League comes off as a bit strange. Also, what the heck determines rank in this region? When characters say, "so-and-so is one of the highest ranking members in the region!" I have no idea what they mean, because what ranks even do isn't really clear. Are there ranks for citizens? (eg. street rats and criminals are one rank, normal citizens another rank, trusted citizens another rank, similar to the world in The Curfew). Or do they mean ranks in the government? If so, what kind of government is it? Corrupt or benevolent? Democracy or dictatorship? How exactly does one "gain ranks" in the government, by becoming a gym leader? And what benefits do you get from being high-ranking (other than the police letting you into closed areas I suppose)? You don't have to give the players all of this information as exposition, but you should figure it out, and then make it apparent through what the players experience in their gameplay. Doing this will make your world feel real.
-This is more of a question... does Contrary actually work? It's probably a problem with the engine you are using, but I can't tell if Contrary works because when pokemon use growl, tail whip etc on my Snivy, it still says the same text. I'm not sure how much you can do to fix it, but I still can't tell if my ability is working, or if I should've chosen a different starter.
...well, I just read the first paragraph of the first post, so now I understand why the gym leaders are as they are. You should be careful to make sure to balance being faithful to your community, with making a game that's actually fun to play.
Well, that's all I can think of to say. Hope any of it was helpful. Good luck with this project, I think it has a lot of promise!