Another change/downgrade from 2012 to 2013: According to the Trek website, only the 2012 models -- not the 2013's are "Fender Ready"...

From looking at the website, it seems that the 2012's and 2013's are both the same price, but the 2013's have:
-- smaller frames
-- smaller diameter tubing
-- a bottle mount was eliminated from the seat tube
-- fender mounts were eliminated

Have there been any other changes/downgrades?

For me, the smaller frame size could be a problem: I have scoliosis and, unlike most riders, an upright seating position gives me a back ache. I need to stretch out a little and form a triangle between the seat and handle bars to provide support for my back. When I'm sitting up straight I can't do that and my back muscles start to cramp up.

Also, I go through a bottle about every 10 miles: only one water bottle just isn't enough for me...

And, I am thinking of a DS as complement to my road bike that I can use in wet conditions -- so I wanted to mount fenders...

So, for me, these are NOT good changes!