He seems to be more of a day-racer to short tour specialist, more like a new Valverde. Mind you, so was Thomas before last year.
I always knew Thomas was a potential GT winner from early in his career - I said (to anyone who would listen) when Sky launched that they should focus on him rather than Wiggins. His problem was that because he was brought up through the BC system with its focus on Olympic medals, he wasted too many of his prime years fannying about on the track. OK, so that might partly have been wishful thinking but once he put his mind to it, and really started to believe in himself as a top road racer, he came good for me. Of course, he also had a huge amount of luck with other elements of the race going in his favour last year - but no one ever won the Tour without a bit of luck on their side.
Alaphilippe has had that luck so far this year, with Froome out, Quintana and Nibali passengers, Pinot having his standard bad day to lose time on an innocuous stage, and no other stand-out contenders. Thomas seems to be a diminishing force and Valverde is looking positively geriatric.
He has only been a one-day specialist and stage hunter so far because that's how the team is set up, but he clearly has the raw talent, and is a genuine all-rounder. He also has a pure racer's instinct. All it will take for him to win a GT is applying that instinct to a different style of racing (ie looking at the long game rather than individual stages) and getting a team of first-class GT-specialist domestiques to support him (and maybe a DS who understands how to win a GT). As others have said, a bit of altitude training probably wouldn't hurt either.
I'm rooting for him to do it. (Although I'm a bit torn because I also want Pinot to win. Those two on the top two steps of the podium would make me very happy in either order.)