Heya, this might the funniest Pokémon fangame i've ever played. In fact i created an account just to post here.
The reason for my coming : DNA Reversers are game breakers. When a mon from a slow experience group (with a high exp per level count) swaps to a mon from a faster experience group, the mon gets a fair amount of levels from the reversion alone. Since fusion doesn't take in account exp but only levels, you can pretty much do loops of
DNA Splicer (slow exp mon as body) >>> DNA Reverser (to fast/erratic exp mon) >>> Super Splicer
... To get low-effort exp for $1800. Which lets you get a level 100 mon before your 5th badge. Which in turn, lets you make about any mon you want level 90 using Super Splicers. Cool way to get to get to level 100 in post-game. But i think you think that breaks the entire point of balancing difficulty for the rest of the game, and i'd have to agree if you do think that.
That, and Wonder Trade.
You can train that Mt. Moon $500 Magikarp into a Gyarados ezpz since you're no longer plagued by ungodly stats, slow exp group, and splash. Wonder Trade that, and since the Wonder Trade uses the BST of the mon you trade to generate the mon you get, you can get endgame stuff before even fighting Misty. I can testify that the Feraligatr/Zapdos fusion i got the first time i traded a Gyarados was as brutal as you'd expect.
And... that's all i can see in terms of game breakers, so i leave that here.