From what I hear, the XR400 is a stump-puller. I've got a 250 MXC, and I can tell you that you will LOVE the weight difference. I went from a DRZ400E to the kTm. The lightness, the suspension, everything about it just made me smile. It is a well-built machine that needs next to nothing to be race-ready and bullet-proof. The diff between the MXC and the EXC is in the tranny (and the lights, I don't have'em). The MXC has the close-ratio tranny, which was a bit of a concern for me at first, what with this being my first 2-stroke and all, but I have quckly grown to love it. I am a bit faster in the woods now, and have learned how to work the clutch to my advantage. As far as your original question about the WR tranny, I think that lower first gear will really be a benefit in the tight stuff, especially if you're a beginner or novice, like myself.
Overall, I think it's a tough call. The XR is heavier, but still a very capable machine. The kTm, IMO, is a woods weapon, ready to get it on! I don't think you could go wrong with the 250 EXC.
Again, this is all just one spode's opinion! :)