You've gotta go with disc brakes if you want the winter dream bike! My Muirwoods 29er has seatstay mounted disc tabs, but it also has a braze-on just above that on the seat stays, which makes for a nice rack/fender mount point. Unfortunately it has vertical dropout, and its near twin, the Hamilton, doesn't have disc tabs.

One thing to ponder, if you're planning to switch between skinny tires and fat tires, there's going to be a limit in your range on a single wheel. The rims you get with a 29er are likely going to be too wide to take a really skinny tire (not less than 32, to make a guess), and I would guess that a rim that will take a 25 wouldn't take Big Apples.