My number one complaint is still (unsurprisingly) the camera system. I've written shedloads about that, though, so I won't talk about it now.
Elements of the story aren't presented strongly enough, and it's something they could have avoided. For example, I've heard a number of people complain about the Prince's actions when he and Farah first reach the Hourglass - they said it wasn't in keeping with the character they'd come to identify with, that they wanted him to do it and he didn't and it broke immersion. The two leads have built up a trust and chemistry over the course of the game which the Prince seems to completely ignore with that decision.
The second time around, I notice the clips in the vision sequences where we see Farah looking.. not entirely trustworthy. So I'm getting the feeling that that was the designer's intention - that the Prince does what he does not because he's failed to build trust, but because what he's seen gives him doubt as to her intentions. The more he thinks about it, the more of a possibility it seems - "You have every reason to hate me," he says to her.
The problem is that the doubt is not made clear enough beforehand. We've had the Prince comment on the visions before; why not now? You'd think that after getting comfortable with this girl ("I will marry her") he'd find these suggestions of possible betrayal really quite worrying. It'd also provide an excellent opportunity for him to expose more about the nature of the visions, for those who haven't already worked it all out (that they only show one of a number of possible futures, not necessarily the one that plays out). Has Farah been disloyal all along, or is he going to do something to cause her to betray him? A whole field of emotional development is opened up. They'd want to introduce the idea earlier, but allowing us to see his doubt about Farah festering would make his hesitation in the Tower of Dawn infinitely more believable.
Another thing I only figured out this time around, is the thing with the sand tanks on the dagger itself. I mean, I know what they are and all, and I knew what they were when represented on my HUD - but I didn't realise that they're actually drawn on the dagger as the yellow part (the blue part being the blade). That's why the Prince can't rewind Farah's death - he looks at the dagger and the sand tanks are empty. That could be made more clear to us. (The 'blood' on the dagger in that scene also looks shite, but that's not so important because we do at least know what it is).
Third underplayed story element: The vizier's state of health. We see him coughing blood near the beginning, and he dies with the words "I could have been... immortal..." so it's pretty clear what he was going for, looking back on the game at the end. Even so, it's something they could have made a lot more of - for the 'big boss' the Vizier hardly even appears in the game. What's he doing all the time the Prince and Farah are making their way to the Tower of Dawn? Why does he need the dagger, anyway? There's a reference near the beginning to his control over the sand creatures - "I knew those winged beasts had a master," the Prince says as he watches the Hourglass being flown to the Tower of Dawn - nothing's made of that. The result is that the player really doesn't care all that much about the Vizier when facing him at the end - I mean, sure, we know he's evil and all, but he's not been causing trouble for the player over the course of the game. They could have gotten him much more involved, get the player really hating him by the end. All it would take would be a short scene inserted before a battle, with him watching them from the Tower (or perhaps some kind of magical device), and doing something with his staff. Suddenly, the battle isn't quite so random - the player makes the connection that the Vizier has sent these creatures to kill us, that he is trying to get rid of us. That would make beating him all the more satisfying; and yet, the gameplay's more or less exactly the same.
Time I got off story elements...
The other thing I don't much like is the gratuitous linearity present in much of the game. I mean, sure, it's a linear game - something I don't take issue with - but in some places it's so obviously scripted to keep the player in one tightly-laid channel as to break immersion, and that's where I've got a problem with it. The most frequent culprit was stuff involving ledges; you've got three ledges at different heights that you have to inch across, but it's set up so that parts of the ledges collapse when you get near them. Even if what the player initially sees is giving them a choice (three ledges) what they actually *get* is only one path. Giving them that kind of freedom and then taking it away is worse than never giving it to them in the first place - for most of the game, I easily accept that the path I have to take is the result of (a) the palace architecture and (b) the damage done since the sands were released; it's the result, most of the time, of things 'bigger' than me. While the ledges just feel like I'm hitting triggers. Needs revising.
Anyway, I should get to bed...