Alright; I did a thing.
Basically, the abilities "Run Away" and "Klutz" are completely removed from the game, and the Pokémon who did have it, now have their hidden ability instead, if it existed in Gen IV. For example, Eevee now has Adaptability and Anticipation, and Ponyta now has Flame Body and Flash Fire. I made an exception for Aipom though, as they'd lose the ability Skill Link upon evolution if I followed this rule. Note that this will make the Raticates you find in numerous dungeons quite a bit harder, not only do they no longer run away from you, but they also have Hustle which will add 50% to their physical attack.
Another thing is that I've made it so that Abra no longer loses the ability to float over water or lava when they evolve into Kadabra and then into Alakazam. I have no idea why it wasn't like this beforehand, especially considering all of Alakazam's sprites show them floating!
Lastly, Castform's size has been reduced to 2 stars instead of 4, Gyrados' to 3 stars from 4, and Milotic's to 3 from 4. I don't believe Castfrom is overpowered like the devs evidently did, especially considering he's damaged by sandstorms. As for Gyrados and Milotic, as they're both non-legendaries who evolve from 1 star Pokémon, I think 3 stars is more appropriate. Interestingly, even though there's no Pokémon in the game who already has a size of 3, it works just perfectly and how you'd expect.
So, yeah. I've done some testing with it and it all seems good. I think I edited both the male and female of each species, but let me if now if I missed anything. I didn't have a patch because of the various regions, and you may already have filled in the portraits with SkyEditor or changed the ROM in some way, so I'll just leave the files. https://drive.google.com/open?id=0B1-sBoZAiZiGdThBRS1iTVpYQlU
To patch a ROM with these files, just download this, and follow this until the "romstats" folder appears, open it, and drop the files into "pokemon_data". Then hit "3a_CompileEverythingAndMakeRom.bat" and the rom.nds is your patched ROM.
Of course, it wouldn't have been possible without @psy_commando's tools, I just made this to show off what they could do.