The built in loader stand on the JD is nice when you are taking the loader off, but it gets in the way for storage. If I take my Kubota loader off in my garage, I can park the tractor right back under it, and lose very little space. The JD arrangement also gets in the way of any front mounted implement, or even weights, etc. You have to take all that stuff off before you can mount the loader. The other thing that I've heard mechanics complain about is that the loader receiver parts (that remain on the tractor when the loader is removed) form a loose connection with the loader after time. I like some things about the JD loader, and I do like their pin arrangement for the quick attach bucket, etc. but overall I have found it very little work to drop, and pin the two "legs" that support the loader when it is off the tractor in exchange for the rugged, and well designed loader. I spent the extra $200+ for Kubota's bucket QA, and still like the JD set up better, but I'm not trading my loader to get it.

I have the small B series tractors, but I think the larger ones work pretty much the same way. The other thing I have noticed is that Kubota's loaders seem to be better matched size wise than the smaller JD ones. The 2305 for example can have a 61" bucket, but has the reputation of being pretty tippy with a loader installed. If you look at one, you can see how much wider than the tractor the loader is, and that is where that reputation comes from. Actually, the 2305 is wider, and somewhat heavier than Kubota's BX series, and would probably be the more stable of the two if the JD loader fit closer to the tractor.
Don't get me wrong, I like most JD tractors very much, and woudn't hesitate to own one, there are just some things I like better on both brands.