I've done both-- Miyata Triplecross for about 10 years of commuting, and now a Trek 6700 mtb.

The hybrid was great, but the more upright riding style got to be a drag. For slightly faster riding, the Triplecross wasn't as efficient or comfortable because I was too upright on the bike.

The 6700 is more of a cross-country mtb, and a bit more stretched out on the geometry, but with road slicks I can cruise pretty well into wind, down hills, and mtb out of saddle stuff. Overall, my riding position is more comfortable, and the workout is more transferable to my other bikes. I'm also glad I switched to a Vaude cycling backpack for gear, becuase the bike is much more responsive now and feels better to do commuting/training rides on. The limitations of the Triplecross kept it as mostly a commuter.

Caveats-- not all mtbs are the same, and some had much better geometries than others for my needs. Also, don't "overbuy" on the dual suspension stuff. Just because the market is for "downhill" bikes with massive suspension travel doesn't mean you need 5 inches of bounce for commuting.

Secondly, some of the commuting-specific bikes might be worth a test ride, like the Burley with a triple crank. It's unfortunate that the REI commuter is a single crank in front. It is possible to get a bike that's "too specialized" to a single purpose.

Finally, for all-weather commuting, disc brakes look like a good idea, as long as you feel they're designed in a way that maintence isn't a big deal. Reading the boards, I've heard great things about the Avid mechanicals, but also that the cables can be hard to keep clean. Some are going back to the hydraulics because of this. I just wish I had the discs for wet-weather commuting and better braking.