Because all of the hacking tools were made for those specific games(including Ruby), and as sumwun says, the most usable and "popular" tools make Emerald and Fire Red super easy to hack. There are also new features that have been developed for only Emerald and Fire Red like the Gen 7 Battle Engine for Emerald, the JPAN hacked battle engine for Fire Red, and the MrDollSteak patch for Fire Red.
That or Just use Jpan's hacked engine which is 1000X more flexible than what you seem to be doing.
All though even after searching for about 30 or so mins i could not fin a download for it.
that might just be me though.
Edit: I legit just found the Hacked engine download after typing this Rip. im gonna try to get into that and make some edits to what i have to see if i can help resolve the weighting issue.
Edit2 : i think my lack of knowledge as far as roms go i really showing here
Woah woah not talking about RPG maker that "engine" (if you even want to call it that) is a taboo in the game dev community.
I also think you over estimate the task of creating a game. You already have what would be 90% of the assets, the other 10% is just pokemon tiles.