As stated above, the MT is the newer model of the XR. When they came out, I was excited and considered trading mine in. The finance department thought otherwise and squashed my hopes of upgrading.
The MT has several improvements over the XR. The neutral PTO is one. It also has the linked throttle, which will rev up the engine as you apply pressure on the hydrostat. The FEL is different, and, from what I hear, has eliminated the dreaded floppy bucket syndrome. Thats just to name a few.
If I were you, I'd spring for the MT. That is unless your dealer is willing to drop the price of the XR significantly. I'm very happy with my XR, but wish it had the features of the MT.