There's a theory in fanfic circles, "The fandom creates what the original media lacked". So Fanfic!Sonic gets weird porn, Les Mis gets low-stakes coffee shop AUs with no deaths, Marvel movies get lots of characterization and the heroes spending time together, etc.
Pokemon romhacks seem to follow the same theory. The originals have lots of mons you can't obtain in a normal playthrough, never adjust balance, squeaky-clean storylines that ignore the horrific implications, and are incredibly easy. So those are the things that motivate someone to dedicate hundreds or thousands of hours to "improving". Add every mon, rebalance the useless ones, actually play out the implications of a Hyper Beam being used on a person, make the bosses a serious challenge. If they were happy with the original games, they wouldn't be doing it.
Thing is, making a game is a LOT of work, so someone doing all of that on their own is either going to take shortcuts or finish in 2062. So yes, there's issues.