The Prince's endgame decision to bring Elika Back from the Dead, releasing Ahriman all over again, is treated as a terrible idea... by Elika herself (since there is nobody else to discuss it with). As the Prince himself points out in the Epilogue, his impulsive decision is actually a very logical one in the long run: it's better to resurrect Elika for a small hope of defeating Ahriman for good than give the world a few centuries of peace before Ahriman conquers it anew with nobody left to challenge him. So why doesn't Elika see his point? Because she doesn't care about stopping Ahriman long-term. She is dead tired of her obligation to fight him, but her instilled sense of duty doesn't let just her walk away, like the Prince would have at the beginning. Her answer to this dilemma is a Heroic Sacrifice (twice)—after all, nobody can say she didn't give it everything if she dies. So, she is not pissed at the Prince because he undid everything they worked for for so long, but because he wouldn't let her rest like she wanted to all along. Turns out, Elika is a much more flawed individual than she first appears to be.
For players who felt like the ending wasted all of their effort, there was a solution for them: turn the game off and stop playing. The credits rolled as the Prince carried Elika to the altar. Basically, the game was telling them, "Hey, you can stop playing now. Game's over."
Probably the largest complaint against 2008. You can't ever get killed, because Elika automatically uses her magic to save you, resetting just the current puzzle or combat. You never had to reload the game unless you chose to stop playing. The Sands trilogy had been similar in principle, because rewinding time also allowed you to cheat death; however, it was trickier in practice. You could only rewind a few seconds at at time, so you could wind up too deep in trouble to back out again. Plus the power had limited uses and needed recharging. Screw up too much and you got sent back to the last save point.
The mechanic of Elika saving you from "death" was an intended mechanic to strip away time from reloading saves and having to travel all the way back to the spot you failed, as well as creating an illusion of an unbroken story (so you don't go through earlier cut-scenes, etc. unless you loaded up a save). It as much a Death Is a Slap on the Wrist as the previous trilogy, only that you no longer have to sit through loading, cut scenes, and wading through the same traps over and over. Many people don't see it that way.
Player Punch: Seriously, how often does a game have two gut punches in a row? And just how often is the one in which a beloved character dies the lesser of the gut punches?!
That One Boss: A lot of people don't like The Warrior very much, mainly because he tends to result in a lot of broken mice and controllers due to his Quick Time Event.
They Wasted a Perfectly Good Plot: Has a major Sequel Hook at the end which Ubisoft is not capitalizing on in the least. Following this game was a Sands of Time midquel instead, and while the fans are frothing at the mouth for some closure regarding this game's story, it can be said that they won't be getting it anytime soon. Unfortunately.