I definitely bought John's attraction to Rodney in the beginning. Bemused, and amused, and a little intriqued. Charmed, even though he wasn't entirely sure why. That all worked wonderfully for me, although I saw in your comment that it didn't work as well for you.

But the deepening of the connection between them was given short-shrift, I felt.

It's very odd to me that there was a story in which McKay felt too one-dimensional and screechy to you and I bought him. To be honest, it makes me giggle.