I saw this post the other day and thought about it so now I can answer, I think!
The house system has always intrigued me from the beginning and when Professor Dumbledore told Harry that it is our choices that matter and not our abilities so much, that made sense because right away you sense that the three Gryffindors have other house qualities as well as other students and teachers. Hermione, obviously Ravenclaw because of her intelligence and her zeal at wanting to learn new things. Harry of course has the Slytherin aspect to him, even if it from Voldemort. Ron - well, I really cannot place him anywhere, so he gets Gryffindor for being a family legacy - LOL! You could argue Neville should be a Hufflepuff because he is kind of just there and noncommittal .
But as each book progresses the characters take on aspects of different houses, most notably Neville who is a true Gryffindor in OotP.
I don't think there is a best house or worse house by itself, but people who have been associated with them in the past may have given them a bad name. Harry did not want to be placed in Slytherin and learned to not trust them because he had been told that is what House Voldemort was in. His ideas were reinforced by Snape being so vile to him.
Snape does not like Gryffindor because he associates it with the Marauders, and especially Sirius and James. He thinks of Gryffindors as being haughty and thinking they are better than anyone else. But these associations have nothing to do with the actual house itself.
Snape has Gryffindorish qualities to him as well. For whatever reason he is protecting Harry, and I do not believe it is only for his gain; I believe he has a very strong attachment to Harry, whether it be family ties or what, I am not sure, but whatever it is, Snape feels the need to make sure Harry is safe.
I think everyone has aspects of each of the four houses within them, and it is only their choice that makes them predominantly one or the other, and each house has its good as well as not so good qualities, just as everything in life.
I have written a book and am not sure I even really answered your question - LOL! But the houses are very interesting to dissect and discuss! ladybrandon