I've been in a similar situation for some time. Just pulled the trigger on a Kubota 3901. Both are good tractors and both will do anything you ask them to do.
For the compact market, I got the impresssion that Deere really does not put their best foot forward with their compact/economy line. You don't get a Deere motor and the build quality is just not up to par when you think of the legendary John Deere. Yanmar is tried and true, but if I'm buying a Deere I want a Deere motor. I can't buy something based on heritage and pedigree alone and I think Deere tries to coast on their name and reputation with their compact line, even if there is very little Deere blood in those tractors. You can get into a compact Deere for a little cheaper than Kubota, but Kubota makes a more solidly built compact. Thicker front axle, overall heavier machine, etc.
If I was a big time farmer in Nebraska and I needed a tractor for my 5,000 acre grain farm, I'd consider Deere. If I was a hobby farmer (which I am) looking for something under 50 HP, I'd go Kubota every time. Deere just doesn't have their heart in that market, IMO.