I have the XR series, its the father to the MT3. Not much difference, LS just added a few features I wish my tractor had. I can tell you that the difference in the HP between PTO and engine is likely something you wont even notice. If your running properly sized implements properly, you wont lug the engine. I've hooked up to some serious implements and ran them just fine. I just ordered a snow blower, 7ft wide, that I'm sure my tractor will handle with ease. I hooked up to a large flail cutter this last spring. One of the hydraulic ones, to see if I could use it to chip some stumps, sticks, and other nasty crap on my property. The guy I borrowed it from told me it needs 50hp at the PTO. My engine is only 45. But I used it anyway. Didn't lug the engine at all. Though, it did do a great job, I cannot afford one of my own. And I would suggest using a stump grinder vs a flail mower for stumps!
This thing is a tank!
The ground clearance issue: yeah, I was concerned with that as well. So concerned that when I installed a new sub-frame mount for my backhoe, I lowered those arms by about 3 inches! Now I really scrape the ground! But, like you said, they help to protect the lines, trans-axle, etc under there. It's also a great place to make a skid plate attach, if you're so inclined. I pretty much go logging with with my tractor, on steep hill sides in the forest. Only issue I had was a stick came up and poked a small hole in my fuel line. Easy fix. I still haven't added a skid plate. Maybe I should do so that soon, knock on wood. But seriously, the ground clearance is not an issue. If you're looking to be driving over stumps and rocks and things, then maybe. But you should try to drive around them.
Branson makes a solid tractor. When speaking with my dealer, who is an LS/Branson/Massy dealer, he likes the Branson's over the rest of them. Just for their simplicity. There is no, or not much, computer 'junk' on those tractors. But I came to the same conclusion as you, they are mechanical and because of that, rough. Simple and easy to work on, but limited in features. LS seemed to fit the bill, for me, well. Comfortable, powerful, loaded with features that are standard, with an inexpensive price tag.
The only thing I'd ever buy a Kubota for, is their resale value. There resale value, like the other big brands, hold well. But is it a wash? I mean, if you buy a Kubota for $60K, sell it for $40K in 5 years. Or buy an LS for $40K and sell it for $20K in five years, are you really gaining anything? (*prices are for demonstration purposes only, not based on actual tractor value or resale value*

) I do not believe that Kubota, John Deere, New Holland, etc are any better or worse than LS. In fact, LS makes tractors for New Holland sooo....
One thing to consider with the other bigger brands is their dealer network. There have been some issues with LS dealers, parts, corporate, etc. But I've never personally experienced them. My interactions with LS have been solid.
In all, get what you believe will work best for you and your budget.