Having owned a few of those and seen many more in my workings, that's quite a write up.
My observations.
Kubota's always have small cabs, if you are a big guy, you'll notice it. Otherwise, not an issue.
The NH/Case has BY FAR the best FEL and bucket set up. Fast, strong, easy to see and quick to run. The kubota has a weak quick attach design. The JD has a poor bucket design and most every JD I've seen (maybe they have fixed this) cannot uncurl and lift at the same time. Not a problem until you try to load something tall (like a dump truck/trailer). Up. stop. uncurl, stop, up. stop. uncurl.stop.up. STUPID. Also, many JD's are a proprietary quick attach so you can only use JD attachments. Which pretty much defeats the point of a universal quick attach.
My neighbor has a 55hp JD (4xxx, i dunno) bought the same year as my NH. I have a NH TC45 (45hp). My loader will lift exactly 1650lbs of fertilizer on a pallet. His noticably bigger tractor will only lift 1500lbs of fertilizer on the same pallet, same forks. His just as expensive machine does not have extensible link arms. This is a 35k dollar tractor, there's no excuse for it not to have extensible link arms.
None of the 45hp cab machines make much in the way of PTO HP. You lose 5hp to the HST, you lose 5 more to the A/C. If you live at altitude, a turbo is a must, otherwise, not really an issue.
Had a MF 1433 (same thing as the 1533, now 1633 just earlier model). Most reliable tractor I owned. I abused it just as hard as everything else and the only thing that broke in 500 hours was a $80 PTO switch that took 10 minutes to replace.
The NH/Case has a weak 3 point. Oh, it lifts it all right, it also bends the arms and stabilizer bars over time (side to side, not up/down). (for the same implements that the 33hp MF handled fine). cheap made in china pot metal and poor castings.
I've never noticed the 2 speed hydro on the NH/Case being a problem. turtle for working, rabbit for transporting. flip back and forth high/low within the range with the button on the FEL joystick. Never an issue. The whole point of a HST is to NOT be shifting.
The Kubota system of pedals is different but in 10 minutes you'd never notice it. You simply don't use brakes on HST 99% of the time, you just hit the other pedal.
I honestly don't think you can go wrong with any of them. You are way over-thinking it.