David, as others have said, you'll probably be happy with either one...I went thru the same search as everyone else and I chose JD over Kubota; especially in the size tractor I wanted I felt the JD was a nicer machine.
Just wanted to respond to something that Bird said in his reply, the fact that a Kubota rep came out to the house to fix something, is nice, but just because JD would prefer that you went thru your dealers for repairs (as opposed to contacting the home office directly) is not necessarily a negative for Deere (in fact, one could argue that if you were unable to get satisfaction from your local Kubota dealer and were forced to call the home office each time something came up, that would be a negative for Kubota).
I had a minor problem with my JD rig shortly after delivery (a part fell off) and my local JD dealer came right out to my house and fixed it up no problem, no charge (80 miles round trip), whereas with my local Kubota dealer (where I used to get my Yanmar worked on), is only 10 miles from my house and the wouldn't do any work at my place, but would happily charge me an arm and leg to haul the tractor back and forth for even minor repairs.
I guess it really depends on the comfort level you have with you local dealer(s). Either machine will be fine. I went green and don't regret it.