At one level, I suppose the Master's insane psycopathy makes sense; but it doesn't make for a particularly effective storyline for me. The idea of ageing the Doctor was explored in The Leisure Hive and we didn't really see anything to add to it here. I'm presently reading Francis Wheen's How Mumbo-Jumbo Conquered the World and the idea of "tuning to the psychic field" is right in its line, something RTD claimed earlier in the series not to do - I think it was after The Shakespeare Code where, commenting on the idea of witches, he said that everything in Doctor Who had to have a rational explanation. And that's rational, my foot. The Captain Jack / Face of Boe idea was a neat (but not particularly convincing) tie-up.
I like the cliffhanger - but what about Clive's photograph from Rose? Didn't that have Eccleston in it? My own favourite idea for a Titanic story would involve the First Doctor, Ian and Barbara - with the companions fretting Aztecs-style about wanting to change history. You can just hear Ian exclaiming: "Well what are we supposed to do, Doctor? Re-arrange the deck chairs?"
So, my run-down of Season 3 probably goes like this:
Human Nature / The Family of Blood (decent plot in its own right, nicely set and a clever tangent on the story arc); Blink (just plain clever); Daleks in Manhattan (well I liked it!); Utopia (I Clavdivs in space!)
Evolution of the Daleks; The Shakespeare Code; Gridlock
Smith and Jones; The Lazarus Experiment
42; The Sound of Drums / Last of the Time Lords
As a whole, probably the best season of the new Who so far, though the best individual episodes probably don't top last years best for me.