When we looked at tractors we ran into the same issue with the gearshift lever location Kubota chose. To put it bluntly, it looked old fashioned and kind of silly. It was the one, major thing I didn't like about the Kubota. But we still went with it.
Now that we've run the Kubota for 60 some odd hours, the location doesn't bother me. It is very easy and intuitive to use the gearshift. Ours is a
M6800, so the cockpit might be a tiny bit bigger then the M4800. I'm also short (5' 6"), so I have the seat moved up a bit.
Getting on and off the tractor is very easy as long as the gearshift lever is in neutral. If it is in gear, my leg will bump the lever on the way out (it never touches it when it is in neutral). I think of it as a safety device. If I put the shuttle shift in neutral to stop the tractor, set the brake, and then try to dismount while the gear shift is still in gear, my shin will bump the lever. I sit back down and put that in neutral too. Most times, I'll also put the high/low range selector in neutral.
I don't wanna get run over!
Try mounting and dismounting the M4800 a dozen times. If you find that gearshift lever to be too big a pain, then the John Deere will be a better fit. Both are great tractors, you just need to figure out which one will fit YOU best.