I believe the new MT's come with the 30.5cc engine now as well. They are geared lower to pull the extra weight. The MT has dual steering servos to turn those big tires. I upgraded my single steering servo on my XT and it still has steering issues on certain terrain. It's a lot of work on that single servo.
Ground clearance is another significant difference. XT has 4cm, MT has 7cm if my memory is right. The wheels on the XT are the same size as rear wheels off a Baja, so with the addition of some XT to Baja adapters, you can buy some Baja rear wheels and put them on your XT with little to no difference in clearance and handling (aside from the tread on the tires).
There are more after market parts available for the MT mainly because it's an older model.
The one thing that basically sold me on an XT is it's power to weight ratio. Same engine, 10lbs lighter.