I'd be pretty shocked if P5 didn't have two protagonists, but we'll see.
My only problem with having multiple protagonists is that it splits up the resources and you risk diluting impact because you have to make sure its tailored for both. I trust Atlus could do it well (as they did in P3P), but personally I'd rather have one protagonist with one extremely dense and well written story. Honestly, I'd be fine if the only path we had was a female. It has nothing to do with gender preference, just fear for lack of focus.
I'm fine with whatever they do though, I pretty much have no internal "rules" that I think Atlus should go by. I trust the team, and I just want them to make something with passion. One problem fans of entertainment have is that when we focus on sequels, we get too specific about what "is" and "isn't" the right thing to do in a series. We often ruin for ourselves what is otherwise perfectly fine content.
It's the ultimate drawback to sequels: each subsequent game carries the weight of an increasing amount of scrutiny and expectation. Add this to the fact that nostalgia skews positive, and it makes sequels have a real tough time getting the benefit of the doubt.