Those are great points. Without Hermione with them in Gryffindor, Ron and Harry would probably have either gotten expelled or flunked out of school ages ago. They'd definitely be missing a vital bond of friendship in her, too.
Another thing that occurred to me is that perhaps Ravenclaw would have been too much of a good thing for Hermione. Maybe she would have become so obsessed with brilliance and academic honors that she would have lost touch with people from an early age, and become either a snob or a very lonely individual. Maybe the Hat thought it would put her in a place where her gifted mind could get more real-world practice and interaction with others.
What I said doesn't make sense! If that were the case-if the Hat knew that some students were susceptible to constant influence of other students with their same or similar personality traits-then surely it would've known that Slytherin, combined with Lucius' Dark background, would be far too much influence on Draco Malfoy.
Oh, well. There goes that theory.