Yeah the Phillies just never had the players to do it really. Franco can't play middle IF, Hernandez apparently can't play 3B, and Kingery was probably meant to get more looks at 2B and OF, not be an everyday SS. And then of course they signed Cabrera, another guy who could play a lot of positions but none of them well.
I think that's the one drawback with Marwin Gonzalez too, he is a bat who can play a lot of places but he's not strong defensively at the more challenging spots (3B, 2B).
I still wouldn't be surprised if Machado and Segura play mulitple positions this year though as you note, as long as Cesar is here things are pretty set.