So I have no trouble believing that Peter fell for MJ for her personality rather than her looks. Especially since we literally saw that on the page. At first, Peter was attracted to MJ but only loved Gwen, and found MJ too flighty and shallow to be really worth his while. But after Gwen died, MJ revealed unexpected depth and kindness when she stayed to comfort him, and it was that emotional connection that was the real beginning of their relationship.
I might be able to buy that if the character in the comics didn't seem to spend most of her time lounging around in Peter's apartment, in nothing but her underwear.
She's certainly never been portrayed as a ditz
, but I don't see her being all that deep or complex either.