Well as long as you are going to change some of the moves that Pokemon have, I have a few more suggestions...
(Actually, this post ended up MUCH longer than I originally anticipated, so only read when you are in the mood to read an essay post)
Croagunk/Toxicroak should be able to learn Earthquake (they can in the official games). They should also be able to learn Bulk Up to try and help out their mediocre defensive stats (Also since you replaced Bulk Up as a TM)
Kingdra should be able to learn Rain Dance, as the majority of its attacks are going to be based off of its special stat and it would also help to activate the Swift Swim ability. It should also have access to Dragon Breath and maybe a few good physical moves, as it has Dragon Dance as a move it learns (Which helps out its speed and attack...too bad it really doesn't get any physical moves)
Froslass is a more of a defensive / support pokemon than an offensive sweeper. I would suggest replacing some of the gen IV moves it learns upon level up that are not in this hack with moves such as Thunder Wave, Spikes, Taunt, Trick, etc.
Charizard has a whole slew of moves it could learn upon leveling up to suit its offensive nature. Sunny Day, Belly Drum, Dragon Dance, Rock Slide, Double-Edge, etc.
Steel Wing for Scizor please.
I would also suggest you buff Rock Smash and Flash. The former could do with a power boost (maybe to say, 50 base power would be good), and Flash should have its accuracy increased to 100% (its a freaking accuracy lowering move and it has low accuracy itself? Makes a lot of sense. </sarcasm>)
This is just from the Pokemon I used. Honestly, the lets play done by DoesntKnowHowToPlay, as well as his post in this topic, demonstrates a pretty glaring flaw of this hack, that being that quite a few pokemon are pretty useless, either because they don't get any good moves, or they get moves that are in the complete opposite spectrum of the role they are supposed to fill. I would suggest going to smogon.com to get a good feel for what moves are good on the Pokemon you put in this hack, as well as Bulbapedia for a list of which moves each Pokemon can learn and from which generation (you could add new moves to each Pokemon via what moves they learn upon leveling up to certain levels that are not available in this hack). Granted, this would reduce the usefulness of the Day Care in the game, but seeing as how so many Pokemon are not available to breed with to get the really good moves, I doubt many people would care (Honestly, a really cool change to the Day Care that would get it to see more use from players would be to make the baby pokemon always be a shiny pokemon)
Finally, and again DoesntKnowHowToPlay brought up another good point, if you want there to be good challenge in this hack (Which definitely seems to be the case), then you shouldn't be giving Golems Flamethrower and level 40 Floatzels Sonic Boom. Giving nearly every single Pokemon Double Team, especially frail Pokemon who really do not really have any time to set up, is bad game design as well, not to mention just gets plain boring to counter, as all you have to do is just use a move that never misses (Like Aerial Ace and Shock Wave, which the player receives just by playing the story) and Double Team becomes pretty useless. I should also mention that according to DoesntKnowHowToPlay, you gave a pokemon Choice Band, but gave it Double Team as one of its moves. If you are going to give a pokemon a Choice item, do not give it any non-attack moves. I'm not saying not to use Double Team, it is a very effective move on the right pokemon, but use it on Pokemon that can take hits well or resist a lot of types, like Kingdra or Scizor, and don't abuse the move. I would suggest taking a look at all of the "boss fight" trainers' Pokemon and consider whether or not their move sets are appropriate given their stats, abilities, and what level of difficulty you want for whatever part of the game that the trainer is at. Again, Smogon is a good place to put together effective movesets (Although considering how derpy the AI can be sometimes, some movesets might be less effective than others).
Soooo yeah, that was a mouthful, and I know that would be a lot of hard work, but it would really improve the core of your hack, as I felt this was one of its biggest flaws. Please consider it. I could try and help you out if it would mean the difference between you doing and not doing this request.
I also come with a couple more design flaws...
-In Sinister Woods at the area past the two strength boulders, it is possible to get yourself stuck with no way to get out (accomplished by pushing the right-hand boulder down as far as it can go).
-In the Mineral Cave accessible by falling down from the Gym in Boulder City, there is a Rock Smash boulder in the way of your path. It is more than possible to go down there without a Pokemon that knows Rock Smash, nor a Pokemon capable of learning Rock Smash, making it impossible to go on without killing off all of your Pokemon to restart at a Pokemon Center. I would suggest removing this boulder as it serves no purpose that I can see.
-Just a personal pet peeve of mine, but it kind of bothers me that Kevin ends up with two fire type pokemon on his team, as it makes the overall typing of his team a little un-balanced. Then again I do love Arcanine and Charizard, so I don't really know what to suggest here. I also felt that Ryan and Light should've had a sixth Pokemon added to their team as well, since Kevin got a sixth one. Just personal preference, do what you will.
-A couple of text errors during the final parts of the game at Dragon Castle.
"Thir actions almost brought the region to collapse."
*Their actions almost brought the region to collapse.
"Did the Pokemon asked you to catch them? Did they asked you to fight their own kind...?"
*Did the Pokemon ask you to catch them? Did they ask you to fight their own kind...?
"Each Island had a strong empire, and both are on war against each other."
*Each Island had a strong empire, and both were on war against each other.
-The sprite that appears on screen for Pokemon when you choose to make them surf sometimes has a glitchy palette.
-The animation of the doors of a house opening up cut into the houses at a certain town (but I sadly can't remember which one at the moment).
-Apparently if you collect three of the four Dragon Gods, there is a chance that Rayquaza won't fight you, even though he should, and this also causes Chaomega to act as if you have never met him before (he will tell you to go see Giratina in Shadow Valley).
-The animation of the protagonist watering a spot where berries can grow with the Wailmer Pail uses the original R/S/E sprite.
Some other suggestions to add to the hack...
-A guy somewhere in the Hevah league that sells held items like Leftovers, Choice Band, Bright Powder, etc.
-Pokemon that hatch from eggs are always shiny (would give more incentive to use the DayCare, plus a lot of the shiny Pokemon, like Charizard, look cool).
-Maybe replace some of the useless furniture items with far more useful battle items from gen IV and V such as Burn Orb and Choice Specs (which could be acquired from the guy in the Hevah league that sells you held items)?
-Rewards other than Nuggets for every mini game available (not that you should not have a Nugget available as a reward in the mini-games, just not all of them).