Revamping the stat system was awful if you consider battling on something beside an online sim. They flat out overcomplicated the hell out of actual cartridge competitive battling needlessly there. Breeding for IVs and all was bad enough, and making us have to train them like that is just annoyingly unnecessary compared to the old way of just fighting whatever and maxing out every stat.
Contests were ehh; they were probably the best incarnation of contests so far but that whole element of the games is wasted dev time/data as far as I'm concerned.
Don't ever call the Regi quest "fun." That thing was an abomination and quite probably the worst puzzle in any Pokémon game. Like really, who the hell thought it was a good idea to put visual braille in a game as a puzzle for kids to solve?
Cynthia is empirically the best champion; Steven wasn't even the champ in Emerald anyway so if you're trying to support Emerald being the best with your points then this is completely irrelevant.
Emerald having a cloning glitch is non-unique; GSC had one too and I think DPP did as well.
I will give, though, that I did highly enjoy the non-aquatic parts of RSE and it definitely had the best incarnation of secret bases and the battle frontier.
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