The Marin is a good bike and what you've listed as the differences are pretty minimal in regard to the two bikes.

The XT vs XTR is minimal for your level of riding.

The vee-brakes are just as good as the mechanical (ball-bearing) discs, performance wise, for the type of riding you've described. Unless the mechanicals are Avids, then they're better. The only significant concern would be if you would ever upgrade to full hydraulic discs; much better performance, but a lot more money as an accessory. The reason being, if you bought the 2000 model and then decided to go with discs, you would have to make sure the frame has disc tabs (mounts) you would also need disc specific hubs (which the 2000 model probably doesn't have) ...etc. It would cost you a lot more later on if you went to discs down the road. With the 2002 model, you would only need to buy the brakes (calipers and rotors).

My only reason to suggest the 2002 model would be the fork. The technology has improved significantly from year to year in the suspension area. Threadless is the way to go. Not that the threaded fork is bad, just old technology! This would require a new stem as well if and when you upgraded the fork. This may not be an issue for you and for $400 you could get a great fork and a stem.

With all this stated, the 2000 model would be the way I would lean. The component differences aren't significant (not $400 worth anyways) and you may not ever upgrade any parts anyways. If you do, the only limiting factor would be if you wanted to go discs and the frame doesn't have tabs welded to it. Otherwise the 2000 model sounds like a great deal! Plus, take some of the money you've saved and buy a decent helmet and a good pair of cycling shorts.