For the most part, I found the game excellent; certainly a worthy successor to the prior two games. There were a few parts before the ending that I found a little out of place, though, and the ending itself is something I find myself torn on.
[spoiler]Kai Leng -- I don't get it. There were several times when he seemed to use the sword for the sake of "cool points" rather than any sense; in a series that had, up to then, been fairly sensible about things it established, there were numerous occasions when calmly shooting someone rather than flipping about playing gymnast-ninja with the sword would have saved a lot of trouble. The Salarian Dalatrasse, for instance. Again during the final fight you have with him on Cronos Station.
For the ending, I honestly quite liked that a lot of the decisions made prior to it had no impact on that scene; to try and force what you did on, say, Rannoch into something on that scale would to me seem far more contrived than leaving it out. The Catalyst's explanation was, however, lacklustre and kind of undermined the menace of the Reapers, for me; that they were these Eldritch Abominations with no clear intent but some plan beyond human comprehension was a theme of which I was very fond.
Lots of little plot holes, too. The Citadel suddenly moving seemed very abrupt since it happened entirely off-screen -- and why were the Reapers building that beam to the Citadel long before the Citadel ever moved? It can't have been a quick construction job. Similarly, why on Earth was the Normandy in a mass relay jump when the Crucible activated?
The best way I've managed to try and reconcile it in my head was that Shepard was gradually being indoctrinated over the course of the series, with the Catalyst's ultimate aim being synthesis: an end to the cycle that pisses it off so. Constructing the Crucible according to Catalyst/Reaper specification would undermine the point of creating that combination of organic and synthetic life, so it was necessary to maintain the cycle up until the circumstances were right to allow the Crucible to both be completed and activated. Shepard, being the Big Damn Hero of the series, was ideal for this, and in initiating synthesis brought their machinations to an end. Destruction and control represented a last resistance to the indoctrination.
It's not by any means a perfect explanation, but it seems to me a bit better than "Catalyst AI explains the incomprehensible in minutes and then Shepard makes a big explosion". After all, in this interpretation there's no reason for the Catalyst to tell the truth when Shepard reaches it. Not the best route, but...
All in all, a fantastic game. An ending I'm not completely satisfied with, although I can see what Bioware wanted to do with it, but as much as I would have liked the catharsis of a grand finale tying all loose ends off, I can overlook the flawed ending for the sake of the main body of the game, I think.[/spoiler]