That sad smile of acceptance and realizing that he's got tears in his eyes was very well done. His thoughts, too, are exactly the right ones. Saying to himself that he isn't part of their future, that it was just a strange twist of fate that brought them together for a limited time, is deeply sad and starts almost a grieving process.
We've seen this scene a lot, but this one really hits home because its about the future and the paths they will take rather than the present and what he should do. It's always annoying to see this scene be about how they don't feel like they should hang out with people who clearly like them or that they don't belong in a place that people clearly want them, but this one is a realization that he's been scared to have and can't argue his way around.
It's a great execution on the otaku/gal romance stress point, and just another way that this manga is a special example of the genre being done exceptionally well.