I suppose the triple is a personal preference. For me, it's absolutely necessary due to the steepness of the hill up to my house. I would definitely want a compact double (or single) if I were going to use this as my CX race bike.
I've got a nicer pair of disc wheels that I'm going to swap in at some point, just because I have them. As I mentioned before, I've also got BB7's that I could put on at any time, but my plan right now is to wait until the Lyras need new brake pads. That plan may change when I see how they perform in the rain. If they work as well as they do dry and are quiet I might just keep them permanently (my BB7's scream like banshees in a fresh rain). I've toyed with the idea of a carbon fork, but that seems like a bit of a waste.
There are definitely a lot of things that can be upgraded, but I don't think there's anything that really "needs" to be upgraded.