I don't think there will be any major physical changes but more ability changes making Eevee a very Powerful Pokemon. I think it would have the ability to melt into water (Vaporeon), have the blinding speed of Jolteon , and have the incredible power that Flareon possesses.
If there were to be any physical changes I would say that Eevee will gain fins (Vaporeon). It's fur would be able to spike up when angered or threatened(Jolteon). Since it shares a striking resemblance to Flareon I am guessing it would keep it's fluffy tail.
If it were to be named I would call it Elementeon for the simple reason that fire, water and electric power are important factors of the earth making it a true elemental Pokemon
Even though it has the 3 evolution stones I still think it would remain a normal type
But this is just a wild guess.