I was talking to a friend who started watching the show with series five, and asked me, without prompting, if the Doctor had always had that kick-ass theme when he did something kick-ass. I had to tell him it was new, and that I'd actually been eagerly listening for Flavia's Theme to reappear at some point in series five. There were a couple of good moments, like when time slows down in The Eleventh Hour at the end of the Doctor's "Believe me for twenty minutes" speech. I guess it was for naught, however, and the regeneration scene was the last we'll hear of it.
Honestly, I was looking for any old music or themes coming back. I was thrilled when "The Greatest Story Never Told" was used for the recaps to the two-parters, and when "The Runaway Bride" played while the Doctor was fishing shrapnel out of the crack.