I've shopped these as well.
I agree wholeheartedly that Kubota's HST is the smoothest to operate. I also agree that the footpedal (for me) is a little funky to use on both these tractors.
For the better part of two years, I've maintained that the Boomers have the best operator area of any tractor, but now the new 'bota 30 series have one that is equal (except the swivel seat - I really like that on the Boomer.)
The 'bota loader seems to handle combo functions (like lift/dump or lift/rollback) better, but the joystick is handier on the NH.
The warranties are about the same.
A HUGE factor for me are the extendable lift arm ends on the Deluxe Boomers - I'm going to be hooking up a lot of things alone, and this will help. The 10-series Kubota MAY not have them - it was a rolling upgrade on the Grand L's over the past year. I priced adding them later - over $600 in parts alone on an
L4610!
R1's have the best traction, but I understand you can't fill them with as much fluid (=less weight) compared to R4's. I believe the R4's to be easier on sod than R1's. On most 'bota, R1's are standard and R4's are extra $. I know that on the Class III Boomers (TC35/40/45) R4's are standard and R1's are extra $ - it may be different on the Class II's.
Bottom line - they are both good tractors, but the dealer is going to support it. Which dealer gives you the most "warm-fuzzies"? Which looks like the best run shop? Which has the biggest parts department? When you are hanging out and other customers walk in, do they look comfortable or defensive? This should be a large part of what you are considering.
Good Luck
Mark