Please don't pounce on me for this, too hard... but "The Hobbit" isn't really Tolkien's best work. (Which is kind of like saying, "That dish isn't the best one available at this world-famous, wonderful restaurant", though. I for one thoroughly enjoyed it.)

"The Hobbit" was written back before Tolkien's world was properly fleshed out as it is in the trilogy and later on the Silmarillion. It's very much a bedtime story; it only gets complex near the end, when the focus widens into the battle over Smaug's treasure and many more people and places join the narrative. At that point you realize--wow, this story takes place in a larger world. The first time I read it, I found the transition a little jarring; I'd been going along, reading it much like I would a fairy tale, and suddenly all of these other people with other motivations showed up and I had to keep track of them like I would while reading a novel with a much wider scope.

Also, Bilbo Baggins is not a silly name. It's a Hobbit name. So there. :)

As for Bilbo being a Stu from the perspective of the Silmarillion... Hmm... Well, in-canon, "The Hobbit" was written by Bilbo himself, and so of course it focuses on his experiences. It doesn't contain the bigger backstory because Bilbo didn't know the bigger backstory until later. Other characters are written as though they were exactly the way Bilbo perceives them.

I wouldn't go so far as to say that from the perspective of the Silmarillion, The Hobbit is a Suefic; I would say it's a genre-shift fic, from fictional-history to fairy-tale. It's about the same thing as the difference between "Wicked" and the Oz book series, a shift from drama to children's fiction. But the movie's Dorothy... well.