I have a strong feeling that faceshells will return again. There's no doubt they give the Spider-Man head that structure and shape that makes the character look so distinguishable. As Johnny-Oh said, it will definitely give it that "movie look".
Plus, I never knew about faceshells until way after the Raimi trilogy was over. I was really amazed at them but quickly understood why they needed to do it. I'm sure the GA won't know about faceshells either, only really the fans that look into this stuff, so to the GA it won't matter. If anything, having no faceshell may make the mask look too silly and draw too much attention to itself, causing everyone in the GA to realise that previous movies used faceshells.
Thus, my point is, faceshells will definitely return as long as they are inconspicuous, and by that I mean less 'bobble-head' like, as we saw in TASM2.