I don't think Pokemon using stones to evolve i.e. Arcanine, Sunflora will ever evolve passed that. Their genes mutated after being exposed to those stones, and I don't think it makes much sense for them to "evolve" passed that, unless it's dubbed a further mutation. Eevee's PokeDEX entry attests to gene modifications in any case, and I think the idea applies to other stone-evos.
Fossil evolutions seem unlikely, too. Fossils have never gone passed one evolution and I don't think they'll break that trend. I don't think the prehistoric era was too well-known for "evolving" anyway. They were simply wiped out. After that, mammals "evolved" and changed to adapt to the new environment. I don't think in the time dinosaurs would've been on Earth there would have been time for them to adapt passed a certain point.
I like the idea of Plusle/Minun getting an evolution. They were always my favourite cheerleaders :)
Apart from that, maybe Persian could evolve, or Meowth gets a baby kitty form. Can't have enough kitties.
Rapidash could evolve into some Pegasus-like thing.
Farfetch'd could finally get some love.
A calf for Miltank and Tauros, where a male becomes Tauros and a female becomes Miltank (fitting into the X&Y chromosome theme of Gen VI)
All'in all, that last one is the only one I might be half-expecting. I'd like to see a lot of gender-based themes for X and Y, since imo it's more about gender than axes.