Why do people group ODIs and T20Is together?
Prior could definitely be an asset in T20Is, he just happens to be useless in ODIs. Dhoni is incredible at ODIs and useless in T20Is. They're very different formats. I'd have no problem with Prior playing in T20s for England, the standard of wicket-keeping would go up massively for a start.
I don't think there will be huge changes for England, something like:
Keeper (Prior or whoever, doesn't matter a great deal and they can go lower in the order)
I think the batting is the hardest to predict, someone like Stokes could certainly break into it if he makes the mental adjustment and something clicks - his bowling and the fact he bats left-handed would fit into the side nicely. But he's just talent at this stage, his T20 record is rubbish.