This sounds just like my search back in May. I was comparing the same models you are. I already owned a small Kubota at the time and still do. I chose the 5205 for a variety of reasons, but I still like my little "Bota". I remeber thinking I would really like to have the 5 cylinder Kubota engine too. They are smooth, no doubt. But, here are the reasons I went with the Deere.
1. Dealer. They were willing to deal and wanted my business. I upgraded from the 5105 to the 5205 for 1k more, which was worth it to me, because 6 muscular 1,500# beasts of burden might just come in handy in a pinch. They are basically the same tractor, but I sleep better knowing I have 6 extra ponies in the stable.
2. The Deere fit me better ergonomically. The farthest control I have to reach is the steering wheel. I do not have to lean or bend to reach any control. The seat absorbs shock and makes working a bumpy field more comfortable and is adjustable to your weight and height. This reason is very important to me because I don't want to feel like I've pulled a muscle or been kicked in the kidneys after 8 hours seat time.
3. Dealer again. To me, a good dealer relationship is important. You are going to need advice, parts, attachments, etc., after your purchase. My dealer has delivered every attachment I've purchased for free, and has been willing to exchange or refund an attachment if I was unhappy with it. It helps that they are only 7 miles from my home, and on my way home from work.
I have 55 trouble free hours as of yesterday, but I would expect no less from any new tractor. Now, had the dealer situation been reversed, I might have went with the Kubota, but I think I would have chosen the
M6800 over the
M4900 and spent the extra bucks because I think there is considerably more value in the
M6800, IMHO, and in my particular situation.
At any rate, you will wind up with an excellent tractor, which ever one you choose. Go with your gut.