In the Potter books, we see that there is some polarization going on among the four Hogwarts Houses. Supposedly, Gryffindor is for the courageous, Ravenclaw for the smartest, Slytherin for the most ambitious, and Hufflepubb is for the most loyal. Reading of certain parts of canon frankly gives me the idea that Hufflepuff may simply be a catch-all House for everyone who doesn't fit into the other three extremes of the bell curve, as Helga Hufflepuff is said to have accepted 'all the rest.' This has led me to believe that Hufflepuff has the largest population of students, with the other three Houses having relatively small populations by comparison.
But that's just a side issue. My real point here is that, if you want to have inter-House unity, then you're going to need to either randomize the Sorting process or else do away with the House system altogether.
Think about it. The entire culture of Hogwarts is geared toward factionalism between the Houses. Students always sit a their House table for meals; they apparently aren't allowed to go sit with a friend from another House, if they want to. Each of the four Houses can only be entered by use of a password, which can change frequently. This sounds to me as if it is purposely designed to breed a sense of clannishness and isolationism from the other Houses. That is exactly the wrong thing to do if you want the student body as a whole to feel united.
Another issue I have is the case of Slytherin House. Into this House appear to be Sorted most of the bad apples. The only non-Slytherin villain we've seen in these books, really, is Peter Pettigrew, who seems to me to be JKR's token nod to the fact that evil isn't exclusive to Slytherin. I haven't seen a single canon Slytherin student I honestly liked and would want to be best buddies with. If anything, it seems to be the head-case House--if the membership of Bellatrix Lestrange and Tom Riddle is to be any indication. And Snape, while not a flaming lunatic, is pretty messed up, emotionally. You don't see much of that in the other Houses, though I'm sure it exists in canon 'reality' to some degree.
There is an old saying that goes something like, "Fly from bad company and cleave to good companions." The theory is that bad companions will only lead you into trouble, while good companions won't. So tell me--Why, instead of distributing the first-year potential Slytherin children randomly among the Houses, are they all lumped together into Slytherin? Wouldn't it be healthier to give them more of a chance to experience normalcy by allowing them to interact with more normal children who might befriend them?
Granted, they could wind up isolated in a non-Slytherin House, and perhaps the Sorting Hat is already doing its best to distribute as many children as it can to the non-Slytherin Houses; I don't know. Maybe the ones currently in Slytherin are the distillation of the type that Salazar Slytherin was looking for; I don't know. Most of those kids just seem Really Obnoxious, to me. Pansy Parkinson as she appears in the books, for example, makes me want to gag.
Still, I think there is a case to be made for mixing the types of students up more than is done in the books. Force the bookworms, jerks, heroes, and normal but loyal people to all have to deal with each other, just the way they will have to in the real world.
I have seen a theory put forth that the Houses of Hogwarts are comparable to the four elements--Hufflepuff/Earth, Ravenclaw/Air, Gryffindor/Fire, and Slytherin/Water. If you go with this interpretation, the set-up of the school itself becomes more of an alchemical theory, perhaps even a crucible for spiritual alchemy, than an examination of sociodynamics. I am not sure how deeply, if at all, JKR structured the alchemical idea, though I personally think it is a fascinating notion and would lend a great additional depth to the books. I, however, am concerned about the sociodynamic thing, and, while I doubt JKR will actually throw out the longstanding House structure, I will be interested to see how or ifshe intends to bring about inter-House unity in Book #7.