I see why people who saw the leaked plot were complaining about the ending, it is absolutely terrible. Juno has been plotting the entire events of the trilogy, her plan ending with Desmond's (rushed) death and her saving the world. It is the same ambiguous "what the!?" crap from ACII, I swear that the writers for these games are lazy and aim their drivel at little kids.
Anyone with half a brain can see that the endings in the AC games are just rushed random crap designed to 'awe' people. Well they don't. Drivel. Desmond's death isn't even tragic; you get sad music for a few seconds, he tells everyone to run, his dad and friends don't even really seem concerned, and then he turns and basically dies - no tension, no drama, no emotion. Just utter crap.
Juno saves the world, but the question is, how? Why didn't she do it before when her people were still alive? Why does she look the same as before (i.e. a projection) when she is released? What is so bad about her being released? Why does Desmond have to die to release her? Why is it specifically Desmond that had to do it? How did she plan the whole thing, like seriously? The ending is abrupt - after she is released, the world is shown being surrounded by green energy for a few seconds and apparently it is saved, and then the credits roll.
Honestly, WHAT WERE THEY THINKING? Sometimes I wish I didn't finish any of the games; usually the plot within the game is intriguing, but the ending always spoils everything in the AC games. It completely turns me off. You can't even skip the credits, which is just a minor complaint though. Thankfully, you start back with Connor after the credits end and are free to get 100% completion from there. Thank goodness for that.
Also thought Connor would die to be perfectly honest, I was pleasantly surprised that he didn't. Also hugely surprised by the very late on 'Father and Son' missions where Connor teams up with Haytham - I actually found these encounters to be humorous and entertaining. I feel sad when Connor has to kill Haytham, though I thought they didn't do it as well as I hoped - this takes a bit of explaining. When Desmond rescues his father, there is a whole "I'd do it for you just because your my dad" message, and though it's hardly delivered all that excellently, the player immediately gets the impression that a twist on that take will happen between Connor and Haytham. They don't really pursue this, which sucks.
Also surprised Haytham wasn't the final boss. However, I really, honestly can't complain; the final stretch of missions after killing Haytham are brilliantly done, showcasing Connor and Lee in almost a grueling battle/pursuit that eclipses everything else. It is a really well done personal battle, and I guess it does fit given Lee is the one that burned down Connor's village at the start of the game (Haytham was innocent of this).
I really liked the final play between the two; Lee sits in a tavern, waiting for Connor. Both men are wounded severely. Connor sits, Lee stares at him without fear. Connor and the two look at each other for a bit after Connon pulls out a knife and places it on the table between him and Lee. Lee drinks from a wine bottle and hands it to Connor, who also drinks. The two seem to smile at each other. Connor eventually reaches his knife, slowly (wounded) pulls himself towards Lee and stabs him in the heart - Lee doesn't resist. I thought this was the best moment in the game and was fantastically done. In that sense - Connor's resolution is far better than Desmond's.