With John, I am suffering a case of elevated expectations.

Easy to do. He's delightfully ambiguous, to the point where the fanonical insights to character are almost essential to understand him and his motivations in the canon. As adelate wrote above, a good deal of his appeal is his relationship with Rodney, which just makes me smile any time I think about it. The other part of the fun of John, I think, is trying to figure him out.

Well, the city of Atlantis, as SF setting design, ROCKS. I'm just saying.

Totally. It becomes a character in its own right, after not too long.