If you're reading this on Livejournal, stop now! I'll try to add spoiler cuts, but I can't guarantee that they'll work
I wouldn't have minded if Derek Jacobi had stayed on. He's an outstanding actor who can do much with very little.
Beyond that, I don't know. The direction in Utopia was strong but the script was very uneven. It started out pretty poor, with the threat of the Futurekind being particularly feeble. The actions of the one Futurekind character who'd managed to get into the Base That Was Under Siege were so obviously there as scaffolding for the plot that I couldn't believe in them at all. But all those things were just background for the goings-on with the Doctor, Martha, Jack and Professor Yana (groan) ... and his fob watch.
The idea of a bad guy living out a whole life as a man dedicated to public service was a good one - a nice parallel with Human Nature/Family of Blood from which it was obviously a continuation. But I think that would have worked better as a Doctor-lite story focusing on that one man. Generally, I don't think the theme wasn't handled nearly as well as it was in Paul Cornell's story.
For an episode with so much other stuff going on, though, the character development and plot arc of Professor Yana worked very well. We got the reminder that Timelords can regenerate early on, and then we got the slow feeding of hints about Yana's nature: that his academic title is an honorific because he has no formal qualifications (what with Universities being long gone, after all); that he craves admiration; that he has been plagued by something that he considers a brain malfunction all his life, causing him to hear the sound of drums in his head; that he lies about his progress to the people he works for, "to give them hope". Yana is trying very hard to be a good man, and mostly succeeding, but all this time his dark side is there.
It was surprising to see the "to be continued" caption at the end. From the timing of the episode, it would seem to be the start of a three-parter, making it the longest single plot in the new series yet. Audacious. But pointless if it isn't the absolute best that the creative team can give, and while Utopia delivered the goods in the end, it wasn't the absolute best.
The structure of the third season as a whole is shaping up well, with the whole thing being a carefully constructed time loop, or big ball of timey-wimey stuff. I like that. I've always been fond of time loop stories. I also liked that story elements from the previous episodes recur - not just the fob watch disguise but also the loss of the TARDIS.
So he is back. I still can't help thinking that Derek Jacobi would have filled the adversary role much better. Though on second thought, John Simms's energetic performance works quite well.
It's fun to note that a number of contradictory rumours all turned out to be true: that Jacobi would play a good guy who is trying to help the last survivors of the human race; that he would play the Master; that John Simms would play the Master. All true, and as we've seen before in Series 1, all working better than the rumours themselves would suggest.
In all, a shaky start to the episode, and too much extraneous business, but ending quite well.