I've said this before and I'll say it again but I'm menstruating and emotional today and actually have the words because @spurious and I have been talking about it--the reason why mcshep is the pairing of all time for me, personally, is this:
Rodney fundamentally believes the best he will ever get is to be tolerated. That if he suppresses his personality for long enough and does the right combination of Tasks, some woman will decide hes not so bad and settle for him. It doesn't matter if he wants her back, being tolerated is enough, and all he deserves.
His sister clearly reinforces this when she asks him about proposing to Katie Brown, which makes me think this was something his parents said as well.
JEANNIE: You think you're gonna find someone better?
McKAY: No, it's not that.
JEANNIE (laughing): ‘Cause you're not!
McKAY: Hang on …
JEANNIE: The fact that you found a nice girl who's willing to put up with all your many little flaws is a miracle.
He thinks it's a miracle, to be tolerated. "You're no John Sheppard," Jeannie reminds him. You can't have anyone in the world like your best friend (who he's painted, to her, as someone who can have anyone in the world). It has NEVER occurred to him that he could be wanted, or desired, for who he is. Only tolerated.
Rodney proposes to Katie Brown shortly after this likely because his sister reminded him the best he could hope for is a nice girl who tolerates him, and he was like I need to lock this down.
THEN, MEANWHILE. John Sheppard, who wants Rodney so badly. Not suppressed or polished or Best Behavior Rodney, either, but Real, Messy, Selfish, Arrogant, Prickly, Unmasked Rodney. John is, without a doubt, the person Rodney is most unabashedly himself in front of, the person who has repeatedly seen him at his worst, the person with which he totally allows his guard to drop, the person he spends his leisure time with. John has seen him, in whole, and wants him. Desires him powerfully and self destructively and all-consumingly with no hope for reciprocity for literal years.
For someone who believes he is fundamentally unlovable and only tolerable and has never even considered desire as a component in his lonely future--to have the person who knows him best (and a person he grudgingly but profoundly admires and loves and thinks is, for some reason, the Platonic Ideal of manhood and also coincidentally so handsome he could have anyone in the world he wanted) WANT him like that...it just!!! they're so romantic to me