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The only two things that would seriously put me off would be no ways to evolve every Pokemon from a previous generation in the game. I.E. No Icy, Moss, or Electric Rocks, needing to grind for Evolution Items, or really anything that makes catching Pokemon a pain in the ass.
The level curve being broken would put me off too.
Pretty much anything that HGSS managed to be terrible at because when HGSS did stupid shit it did REALLY stupid shit.
I can tolorate not having a Battle Front but not being able to catch or evolve certain Pokemon because of hindsight is a serious crime and no matter what that game did right I can't defend it.