To me, part of what makes the reader able to relate to the story is the Gryffindor vs. Slytherin plot. It also gives the lesson to not judge people based on their associations and your prejudices. Its a lesson that transcends time, if you think about it. And honestly, Harry's comment to his son about being sorted into Slytherin was obviously a joke. If I'm not mistaken, he actually explains that one of his son's namesake was in Slytherin, so that the fact that he were sorted into Slytherin wouldn't be any true indication as to what type of person his son is. I'd have to re-read that (and that was actually one of my least favorite parts of the book).
Furthermore, in the Order of the Phoenix book, a Ravenclaw or Hufflepuff betray Dumbledore's Army, if I'm not mistaken. Dumbledore's Army is an illustration of the unity that occurred in Hogwarts - the unity was done by choice and the Slytherins chose not to associate themselves with the other houses.
The series also shows why some of these people and families chose the paths they did. The Malfoy's were scared to go against Voldormort while Bellatrix actually worshiped him. Fenir Greyback saw him as a means to gain rank and, possibly, use the fear of Fenir and the werewolves to spur a social reform regarding the werewolves (i.e. using their intimidation to Voldormort's benefit which, in turn, allow the werewolves to use their status with Voldormort to gain acceptance - at least that's why I felt he worked with voldormort).
Its quite literally a magical World War 2 - Voldormort being Hilter and the Slytherin house being the Germans which are taught by not only their families (if they consider, like the Blacks or Malfoys, being in Slytherin a badge of Honor) but their schoolmates (the natural fear and hate of Slytherins feeding the Slytherins' dislike and hate of the other houses and natural rivalry of Gryffindor vs. Slytherin). This leads the Slytherins to turn toward Voldormort as soon as they are capable of working in his regime.
I find the lack of true unity between the houses, specifically Slytherin and Gryffindor, necessary.
I'd probably have a lot more to say, but I can't think of it right now and will just end it here. :)