I have had all 3 brands, and several different transmissions. The shuttle shift has always been the cat's meow. It is not crucial, but easier than a straight shift, more power than a hydro. I also think Kubota is built the heaviest, but John Deere holds a big edge on parts. A 3 week Kubota order might be 2 or 3 days for John Deere. I have 2 older Fords, great tractors, made just before the takeover, not sure if newer New Hollands have the same reliability. The parts also tend to be expensive...I would say all 3 good brands. Several friends are fond of their Masseys, as well.
the Kubota M6040 4x4 weighs, 5445#, the Deere 5065E weighs 5070# and the NH WRKmaster 65 weighs 5700#, so NH is the heaviest, great simple reliable tractor, and i dont know where you buy your parts but we constantly have customers switch over from the green parts and buy a NH tractor becasue of parts and service from the green guys.