The 5.2 SL is the way to go if you you are going with a Trek. It is
the 110 carbon with full ultegra which I've heard is more than does the
trick. The SL frame is $3k if you try to buy it on it's own making
the bike even more of a steal. The wheels it comes with aren't as
nice as the 5.9, but they work fine.

I also swapped out for DA kit (sold the Ultegra for $750, picked up DA
for $1050) since I'm an equipment snob. The B-trager trim parts are
fine as well. The saddle sucks, but chances are you already have one
you like there anyway.

I FAR prefer my 5.2SL frame to the 5500 or the 5900 I've had in past
seasons. The rear end is much stiffer and really carves out the turns.

Compared to the Scott, or Giant, or whatever - for the price you'll
have a hard time finding as good a bike, and I prefer the ride of the
more traditional geometry bikes (non-compact).