I have a Kubota L3400 and its a heck of a machine. Haven't had a lick of problems with it and the HST is a godsend doing loader work! The loader is strong enough to lift the rear end off the ground if your not paying close attention. Its a strong lil machine, the only thing I dont like is the HST seems to suck alot of power but I only notice it when I'm running something off of the pto. I have a few thousand hours on an older john deere 750 with a manual trans and it was such a PITA to use the loader on it. I was always shifting gears. I also got a heck of a forearm work out from the lack of power steering! That was a very reliable tractor for being 30 years old though! just regular maintenance on it.
I went with the Deere for two reasons for my bigger tractor. The weight difference was one(deere outweighed the kubota by over 1k lbs) and the 0% financing for 72 months was the other. Would I ever buy a full size Kubota? you betcha, it just made more money sense for the deere at the time.
My best advice would be to go drive some different models of the brands you are considering. You will be suprised at what aggravates you and what is very handy. That in and of itself might make up your mind for you even if its not the cheapest option.