I don't play many shooters. I've played Uncharted plenty, though, and I can't say I ever had an issue with the analog stick placement. It works as it should, and it doesn't hinder my ability to aim. I can see you being uncomfortable with it if you're used to the 360 controller, but if you've used the Dual Shock for a while, which I'm guessing you have, it shouldn't be too big of a problem! Maybe some minor readjustment to get reacquainted with it. I dunno, I can flip between both of the controllers and use them well enough.
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Simplicity is the ultimate sophistication.