I really dig ITMD's theme, and I really dig the episodes in general, but in a perfect world where the creators were 100% positive they weren't getting renewed for a fifth year from the outset of the fourth, I think it would have been better to have placed those episodes earlier in the season. I was really digging the ENT crew in the show's second half, so as I counted down those last episodes, it was kind of souring to me that we didn't really see our crew for two whole episodes so close to the finale.
In such perfect worlds, TPTB would have probably had the time to do something better than TATV, too, since I've read that they tried to get a bonus hour to do a bigger finale but the studio wouldn't budge from their 22-episode deal.
Honestly, expanding the Terra Prime arc into a trilogy would have been an OK idea, with the last hour focusing more on saying goodbye to the crew and ending the threat in the first couple of acts. It's not like ENT Season was a stranger to trilogies!
Ah, er, where was I? Agree with the OP, Gagarin would have been lovely at least.