Before I read this, I would've said PW is the better game. And arguably, it still is.
But I never had really thought about how weak PW story was in relation to PO. I think PO's weakest point in that regard was the presentation of the story. PW had tons of audio that gave the characters more..well, character. PO just had too much story presented as text-only, which kind of takes away something from the characters.
PO also had absolutely no variety in terms of environments, which is a shame as well. Everything felt like a very empty warehouse of some sort. It's a shame there wasn't more variety. But outside of that, I do think the character models are sharper in PO than PW.
The controls in PW, while not fantastic, were more manageable. I can't believe Kojima didn't design either game around a single analog stick ala MGS1/MGS2. PO was made harder to play in that regards, but having played the game recently, I realized how useful the L button is in PO, which makes the game much more enjoyable to play. I disagree with your assessment of using the right analog stick for camera control- since the game has a camera that tries to swing behind the character when possible, it kind of makes to see what you want unless you are actively managing that stuck.
But I do agree with you in terms of story and characters- they are simply better in PO when you think about them and forget the presentation.