I read an article just before I went that said there was originally a lot of mention of Howard between them throughout the film but neither of them were particularly comfortable with the scenes and Joss felt like he was making Iron Man 3, rather than an Avengers film so he cut pretty much all of it. Sucks for Tony/Steve shippers but I totally understand why he made that call and I think it was definitely for the betterment of the film as a whole.