Well to name several I would say certain sections forcing you to play characters you don't want to play as or are not good at, certain people may not like certain platforming sections, many missed enemy opertunities (how the hell weren't there Kirby enemies in a game made by Sakurai, I want Scarfies dammit), fighting Dubor or whatever that boss was that tried to kill Lucas and Pokemon Trainer twice in a row becuase beating the boss twice in a row totally proves you can beat it right?, fighting some bosses (ie Rayquaza for example) making no sense (Seriously I think they could have chose a move malevolent or volatile Legendary than Rayquaza), The Great [tornado fang]ing Maze, the multiplayer of it isn't really polished which I find surprising for a 'party game' like Smash, and Sonic showing up at the last minute since he was a last minute addition and thus had no interactions with anyone and as a result he seemed like a poorly written Dues Ex Machina.
I think that's why people rag on it, but there could be more reasons. I felt it was awesome when it first came out, but I don't think it will age well.