In my opinion, Kubota is the superior product until you get up to large ag tractors, and even then...Kubota is making inroads with machines like the M6.
Weight can be a benefit or detriment. Higher weight helps a tractor handle a heavier implement better, but it also causes the engine to have to use more horsepower for moving the weight of the machine. This is especially noticeable if you mow or till uphill. High weight can also cause much worse rut damage on soft or wet ground. As others have mentioned, you can always add weight but you can't remove stock weight. If your tractor is only going to do one specific function and you want more weight, a Deere might be better from a weight standpoint. But if you want a general purpose tractor, one that is a little lighter might be beneficial.
John Deere markets themselves as an iconic, American company. And they are, until you realize many of their smaller tractors are built in Pune, India. I'd certainly rather have a tractor built in Japan than a third world country with poorly paid employees working in potentially poor conditions. There is no reason for an American company to be building in India other than to exploit a poor country in order to bring in more profit.
Nevertheless, companies like Mahindra are even worse. They either sell licensed clones of other tractors like TYM or even worse sell minimally-upgraded versions of their own ancient designs.
In the smaller tractors, especially HST...the debate over the twin-pedal JD vs the treadle-pedal Kubota has raged on for years. I came from a twin-pedal HST which I really liked and bought my first Kubota HST. For the first 25 hours or so, I missed the twin pedal design. But since then, the treadle design works just fine for me without even a thought and I'm every bit as productive. I think a person can quickly get accustomed to either and there really is no advantage to either. Some people even say it is unnatural on a twin pedal design to push forward to move forward AND push forward to go backwards. The treadle pushes forward to go forward and backwards to go backwards.
JD continues to use a proprietary Quick-Attach design on their loaders. Not only is it not quite as easy to use, it locks the operator into buying JD implements or making modifications to use universal attachments. This is inline with JD's focus on profits over the consumer's best interests. Kubota has used SSQA from the start.
In the smallest of tractors, like the 1-2-3(E) series JD's, the HST transmission only gives you two ranges. This is garbage! A 3-range is far more optimal, matching speed to the implement. Mowing with a two range more often than not forces you into the low range because there is not enough power to move at the faster speed range while mowing heavy grass. Aside from the smallest BX series, Kubota gives you three ranges.
Many of the smaller JD tractors do not provide an engine temp gauge...just a warning light. All Kubotas give you an engine temp gauge.
As has been covered, JD loves a plastic hood and side panels, and plastic rear fenders. I'd prefer metal myself. There's no doubt the plastic sure feels flimsy to the touch.
The Yanmar engine...I'd take a Kubota any day of the week in the smaller horsepower versions. There's a reason companies like Bobcat, Jacobsen, and Carrier tractor trailer reefer units run small Kubota diesels. They are dead-nuts reliable and long lasting, and smooth. A lot of the smaller Deere engines are 3-cylinder. 3 cylinder engines are not as smooth as four cylinders. Deere would rather sell you a 3-banger with a turbo than a 4-cylinder natural aspiration...because it's cheaper. And very interesting how this iconic American company subs out the engine to a Jap company.
I prefer to buy American (US made) every time...but I'm not going to pay Deere more for a tractor with less features that's made in India with a Japanese engine. I'll just buy a Japanese tractor with a Japanese motor and a Kubota made in USA loader.
Don't get me wrong, there are a few things I like about JD. I think they generally have better styling than Kubota. I like the color better, and the paint doesn't fade as quickly as the orange does. But overall, Kubota is the better machine.