Base Breaker: Alister. One half of the fandom find him intolerable, the other half adore him and were furious at his reduced role in Underworld. Oddly, Zip did not receive the same reaction, despite serving the exact same function as Alister, as everyone generally likes him.
Possibly due to simple personality preferences. Zip seems more laid-back and enthusiastic, while Alister tends to be fussier and a bit on the stuffy side, which can be taken as nagging.
Breather Level: After the long Kazakstan and England levels, Nepal is a breeze save for a couple tricky sections.
Evil Is Sexy: Amanda goes through quite a wardrobe change in the period between her believed death and her reappearance in Kazakhstan. Gone are the cute shorts and blouses with flowery embroidery and in come the cleavage-baring tops and tight, preferably leather pants.
It's Short, so It Sucks: A criticism of Legend, which was only eight levels (seven if you don't count the final boss level). That said, some have argued that it's great precisely because it's only eight levels, as the game doesn't get overlong and repetitive.
Stop Helping Me!: General consensus amongst the fandom seems to be that Zip and Alister's frequent comments ruin the feeling of isolation and provide too much help during puzzles, negating the feeling of accomplishment when you finally progress. They have their supporters though.
Arguably the reaction was less to do with story changes (as story was never a big part of the series anyway) but the linearity and lack of exploration or isolation.
There was also some criticism about the game engine change; while many liked that the series got away from the limited "square-based" movement, others found it difficult to adjust and/or found it not as accurate.