I read somewhere that Gero saw a lot of himself in McKay and he thought that McKay should have a girlfriend. So I saw Keller for what she was, a Mary Sue. Of course, I inhaled the entire series in 12 sittings so my view of her is probably skewed. (I really, really don't like the character but that's for another thread.)
However, from the moment we see McKay and Sheppard on screen together you can see there's something special there. When they get to Atlantis and they're going up the stairs for the first time, Rodney is right there at John's side. Even little things like that make me smile. In the pilot you can see that even though John is feeling way out of his depth, he's enjoying those little moments with Rodney - the way he teases him ("720"), those little smirky smiles... Rodney just looks adorably confused but has been paying enough attention to John to personally show him the
Puddlejumpers; most likely to please John and see him light up with happiness.
Of course, I'd read all of xanthe's John/Rodney stories before I ever actually saw the show so I had an idea of what to look for.