I remember hating milktank, gengar, and kingdra when I played it like 7 years ago. I remember the night music around the dragon voss town had a creepy tone, or not, I could be wrong. Also, wasn't saphire/ruby the first game to have two seperate legendaries that you couldn't catch in one game?
Also: I hated some of the modifications from firered/leafgreen, such as how they moved multres to that new cigarette island.