When I was faced with almost the same dilemma (5425 vs M7040) I wound up with the 5425. In my opinion, the cab on the John Deere is better. It is bigger, roomier, has better sight lines, and the controls all fall to hand very easily.
My previous tractor was a Kubota M6800. Before that was two other Kubota tractors. I have no issues or complaints with Kubota. They build a very fine machine.
However, in my situation the John Deere is the better machine. The ergonomics, fit, and finish are as good as, if not better, than the Kubota.
Honestly, you're going to have to drive them both and see which tickles your fancy. If you are doing ground engaging type of work, my nod would definitely be the John Deere.