Were you reading older fics, out of curiosity? Especially Post-Trinity Fics have a habit of writing Rodney as the tragic hero making John out to be a jerk...the more recent trend in McShep fic is that John is pining and Rodney is oblivious, which puts John in a more sympathetic role.

That being said, if you're a Sheppard girl and you read gen, there's a bunch of gen authors who write Sheppard-focused h/c. Check out rhymer23, kodiak_bear, and kristen999, and their flists and recs for more. friendshipper and tipper_green also write gen, with a team focus; John & Rodney are often the center of the h/c but there's no major preference given to one or the other.

As far as McShep goes, crysothemis is a John-fan who writes delightful stories in which they're both complete idiots, seperis is a McShepper whose clear favorite character is John (her SGA stuff can get too dark for me but she's an excellent writer). You should also try sheafrotherdon and aesc (and their co-writing cohorts) as they're talented writers who love both chars and wouldn't wrong either of them.

There's a ton of other great writers in the fandom who treat both chars well, but I admit I tend to go for Rodney-centric authors myself (though I don't like to see John being made the lesser char for it) - I'm specifically reccing you those that I tend to see as more John-focused, because yeah, depending on what parts of the fandom you've been in, you could get the idea that Rodney is everyone's favorite, when he's not...!