You have to remember that currently runequest is a rules system. The idea of attaching middle earth as a setting would be to modify the rules to reflect it, much in the same way traveller has been in some ways to do judge dread, hammers slammers etc., and how D&D 3.5 to do game like Star Wars and World of Warcraft.
While you do make a valid point, I do not see it as an impossible hurdle to overcome. If an RPG were to be made, I would imagine the emphasis with picture and pitching it would be on the movies. While I do agree with you on the Samwise example, in the movie there are plenty of lethal fights, but it is in a different style.
Again, variant magic systems are the idea with a variant license. I think this point you bring up would be the very reason that producing a game of Middle Earth would work, because there is something different with it, while it is similar to other games. Once more, it is something that makes the setting unique. Again, if you were to do a hard sci-fi versio of traveller you would have to do a different section on ships, and if it were D&D and you did 'A game of thrones' you would have to modify the rules to suit the setting, that is the idea of doing a licensed game. That's the whole point of it actually.
In contrast, I am not familiar with the systems you list, which while it does not help my argument, I would be interested to here how they would work better. I am always interesting in learning about new (to me) rules systems.
You have a problems with Mouseguard? I am not familiar with the company. What happened exactly?
PS: You could argue that Samwise would havea high dodge, stealth and throw stat, LOL.