I've had both over the years and have both colors now. I will say that for the utility series 5000, 6000 and up farm tractors and bigger, JD is great. Good and heavy, rugged for tillage and such. The Japanese 790/990 and predecessors are terrific as well. Comperable to a 3400/4400 Kubota.
That leaves everything else to Kubota. Their CUT and SCUT's set the standard for performance, fuel economy, ergonomics and trouble-free simplicity. They just work. At times the bigger tractors are a little light but there are wights if you need them. Loaders weren't all that great but are now.
The only disadvantage to Kubota would be the accessories available and at reasonable prices for the JD stuff. Things like weights and brackets. Kubota is expensive and hard to find.
Another thing that concerns me is the apparent desire by JD to get one dealer to have many stores in surrounding towns, crowding out the single dealer. Kubota wants dealers everywhere. I think that the JD way would keep prices higher and non-competitive while Kubota would be the reverse.