"Twice Shy" is one of those episodes that would have been great in Season 1 but feels very out of place in Season 4. It's very much a filler episode in the middle of the final arc of the series (which more or less starts with "Unrealized Reality"). That said, the last scene of "Twice Shy" is incredibly important!
I was never a huge fan of "Terra Firma." I just didn't like many of the actors chosen to play John's friends and family. And yeah, you can count me as someone who didn't like the 9/11 reference. At that point, we were still being flooded with 9/11 stuff on the news, and I was just tired of hearing about it. The last thing I wanted was for my favorite sci-fi show to bring it up as well.