Rodney thinks he's finally figured it out; at last he knows why his best friend here irritates him as much as he delights him. Sure, he's smarter than Sheppard and has the numbers to prove it. But Sheppard took the Mensa test out of curiosity, to see what it was like. He had passed it and never even bothered to send in the membership paperwork. Later, a long time after the adrenaline of their encounter with Kolya has faded, Rodney realizes how goddamned annoyed he is at Sheppard for that.
Because that achievement meant nothing to Sheppard. Or, to be more precise, it didn't matter to him as it did to Rodney. The strangest things came so easily to Sheppard and he merely shrugged at them. Major 'Ancient gene that only a fraction of living humans possess is in my DNA? I can light up an abandoned alien city like a Christmas tree? Huh, what do you know about that?' John Sheppard.
Deep down, Rodney knows that what bothers him most is that Sheppard's sense of self isn't affected by any of these things. Whereas Rodney needs achievement and acknowledgment on a fairly regular basis or he feels himself starting to fade around the edges, beginning to disappear the way he did when he was a child. Other people merely needed food, water, shelter and oxygen to survive. Rodney needs other people to see him... and what was the point of being seen if you weren't seen as the best?
He is the best, at lots of things. He knows the circuitry of the city as no one else does. He reads Ancient now, better than some of the linguists they brought along. He has built bombs, hotwired space-ships, saved people's lives again and again. But Sheppard is better at the one thing Rodney wants most. John Sheppard can be himself, even alone, in the dark, screaming in pain or laughing at himself. It's not an intelligence quotient Rodney is familiar with and he doubts there is any test but the ones they seem to encounter day after day in this bizarre galaxy. John passes those tests again and again, never blurs, never fades.
Rodney waits for the day that he, too, can be the best at being himself. So he watches Sheppard and he tries to be Rodney McKay as hard as he can, forcing himself into bas-relief. Sometimes, he almost thinks it is working.