Or... rats, now I can't remember who I was talking about this with...but stories where Rodney declares that he's always wanted John but didn't persue it for x reason, and John doesn't fall into his arms, but instead thinks maybe this isn't the greatest start for a relationship, since Rodney was either leading the women on or is maybe leading John on as well.

There'll never be many stories where these kinds of things happen, I don't think, because the McKay/Sheppard people tend to write John taking Rodney in, and everyone else tends to skip over John/Rodney angst most of the time.