The Defiant One: We were not given reason to believe that he couldn't hit the Wraith; rather, he did appear to hit it each time -- if he hadn't, there would have been a hazard to Sheppard, since he was directly behind the target. This did not seem to cause Rodney to hesitate.
Rodney had to be reminded to reload.
Siege, Part 3: Rodney is ready to fire on the approaching Wraith, but accidentally ejects the clip, probably instead of disengaging the safety.
Runner: Rodney's skill was disparaged by Ford -- not his aim in particular, but the likelihood of accidental discharge. Then Ford disarms McKay. Later, Ford returns the weapon when they appear to be under threat, without any demeaning warnings one might expect toward a crappy shot. Then, in a face off, Rodney shoots Ford in the shoulder -- which makes sense if a) Rodney would aim for the shoulder in an attempt to incapacitate rather than kill (as implied by his statement immediately prior, and later while hanging upside down), and b) Rodney can hit where he's aiming. When that doesn't have the expected effect and Rodney flees, shooting into the air looks pretty silly, but it is effective as far as establishing location and danger is concerned, and he's already established that shooting Ford doesn't do a lot of good.
The Long Goodbye: Out of everyone in and near the room, Sheppard turns over his weapon to Rodney. Shortly thereafter, under fire, Rodney shoots 3 times toward Sheppard's body controlled by a hostile alien consciousness,
Sateda: Beckett discounts Rodney's skill, saying "And you're a terrible shot." Rodney doesn't deny it.
Common Ground: Spooked, Rodney opens fire with a P-90 on what turns out to be a mouse. Or perhaps a rat. At any rate, afterward, it is a dead mouse. Hitting a moving target that size is not as easy as it looks. Trust me.
My biased opinion: Rodney has the background, the hand-eye coordination, and enough experience to be a good shot, even an excellent one. A site picture is a site picture, and Rodney hits what he aims at, when he bothers to aim. However, he's not experienced enough with firearms or combat to keep his cool under pressure (failure to reload, clip ejection, losing skill when under fire) or be considered an expert. Knowing that safeties and ejection buttons exist is not the same as knowing instinctively and reflexively which to use when. He may not correct Beckett's misconception about his skill because a) he may feel that if he's not the best in the field, his skill is not worth pointing out, b) protesting too much gives the opposite impression, or c) he gets enough crap from Beckett already from exaggerating his ailments and he'd rather not expose himself to more mockery. I think he gets too much flak in fandom for being a crap shot because a) we're taking Carson's word for it, b) we're equating general weapons expertise with the ability to hit a target, or c) we're being blinded by McKay's own unease. For all that he's never missed when he's aiming, he's also never displayed any significant confidence with weapons.
Details gathered from transcripts at Gateworld, where it's way too easy to see spoilers for much of Season 3. However, I'm not particularly sad about this.
Comments
In The Long Goodbye, I'm pretty sure John's lucky and/or skilled enough not to get shot in the face.
I agree with your interpretation; I also think Rodney can't watch himself killing human beings. I'll have to rewatch again, but he might have been genuinely bothered by the mouse in Common Ground, given his reaction to rodents in Hide and Seek and Duet. And Letters from Pegasus establishes his childhood attachment to cute mammals.
I'd write it off as a quirk after two seasons, but returning to it in the third season makes me think it's a consciously chosen theme.
Much as I would love to think Rodney's actually a good shot but is taking the moral high ground, I don't think that's where they are going on the show.
Almost every time we see him shoot (especially with the P90), he's either a) not looking at all or b) shooting wildly (he tends to shoot one handed and flail around while doing so).
Based on that interpretation, I'd rather not be anywhere near him when he panics and starts firing. I really think Shep was just lucky in "The Long Goodbye," because I really find it hard to believe Rodney would be able to specifically hit the upper arm.
Ditto in "Runner," where I think Rodney was trying to hurt Ford, and then had to deal with the fact that he mostly "winged" him.
But obviously I may be in a minority here. :D
I'm interested to see an accounting of more of the times he's shot wildly. I listed the one that I remembered, and I vaguely recall a couple more that I can't place.