It's just me, I guess. Visual errors bother me a lot. When Super/Hyper Sonic is in any other position than idle, crouching, running or jumping, the sprite reverts to normal Sonic while retaining just the palette, and I always hated this on the vanilla game.
That said, Complete does fix all this as well as other bugs and integrates both halves of the game better than vanilla does, so there's that, too.
And I agree about Complete being better overall than AIR due to ease of use (same for other decomps for Sonic 1 and 2), since they require extremely specific ROMs that aren't even available anymore thanks to Sega delisting them. I hope this makes decomp authors just realize they need to support a wider range of ROMs, as Sega doesn't care for its fans.