Totally agreed about Clint as Hufflepuff and Natasha as Slytherin.

Personally, I'd actually stick all the science geeks - Tony and Bruce and Jane - into Ravenclaw, which is actually also were I see Pepper.

I'd put Coulson in Gryffindor, because while I think his bravery is very quiet, I think it runs strong and deep (and I think it says a lot about him that he picked Captain America to fangirl over).

Maria I'd also put in Gryffindor - she's straightforward and ethical in a way that reads as Gryffindor to me.