I'm not familiar with the JD 5093E but just looked over it's specs.
The Kubota is listed with 84 PTO HP vs. 75 for the JD.
The JD comes with a 12 speed transmission, optional on the Kubota. If you go with the 12 speed on the kubota you also get the extra 3 point lift capability (7000 lbs). The standard 3 point lift capacity on the kubota is higher than the JD.
It looks like the JD has a 540/540E PTO which is not available on the Kubota. 540/1000 pto is available on both tractors.
I think the JD has a mechanical pto actuation while the kubota has a hydraulic pto actuation.
The kubota wheelbase is slightly longer than the JD.
The kubota comes with larger tires standard (12.4-24, 18.4-30).
Check them both out and see which one you prefer.