They sure prefer 3 WR sets--but almost always throw in them. I think they trust Thompkins pretty well, but I guess the element of surprise doesn't make up for the lack of a third option.
Yeah, this is the problem. The 3 WR set with Vereen in the backfield and Dobson / Edelman / Amendola gives the best options for passing, but Vereen is averaging something like 4 carries for 14 yards in the games since coming back from wrist injury. The 2 TE (or 1 TE, 1 FB, 1 HB) set with Blount or Ridley is good for running, but the passing options are lousy.
I don't know if they really "prefer" 3 WR sets. Aaron Hernandez, um, didn't work out, and Gronk missed the first six weeks. They ran a fair amount of 2 TE when he came back, but then Hoomanawanui got hurt and missed three games. By the time he got back, Gronk was on IR. So they haven't really had the personnel to run a lot of 2 TE stuff this year.
The 2 WR set in the first half was Dobson and Edelman; I'd guess Thompkins gets those snaps now because for whatever reason Amendola seems limited--groin still?
Amendola's injury seems to be part of it, but they also seem to be trying to get a traditional "X" receiver going at one of the spots rather than the all-midget attack of recent years. Amendola and Edelman have pretty similar skill sets.