Actually, that's not true. The original Playstation design (after the SNES) included a dual analog controller with longer handles, concave sticks, and a single force feedback motor. That is why you can plug a DualShock in with certain launch titles and still get weak force feedback.
I think the story goes that they pulled it out late in development because they were afraid of infringing Nintendo's patents - something that they later went ahead with anyway and have been in trouble multiple times with different companies for their controller design. (I think this is also why only Nintendo can use cross-shaped d-pads. Sad but true... so most use a disc and Sony uses 4 wedges even though they're all the same inside.)
That's subjective. I find offset sticks weirder and less comfortable than symmetrical ones, wherever they're placed. The XBox layout is sort of like Nintendo's c-stick concept - except the c-stick was never meant for serious use! That's why they didn't put a wide top on it; it's for cameras and menus. That I think is the real habit based preference - because when you're using the same controls on both sides, what's the advantage of having one at the bottom and one at the top?
Convex/concave tops - it makes sense in theory that concave would be better since you could pull instead of push the stick, but since they came in in the mid 1990s, I've never had it make any difference since they're rubberized. My thumb's not concave either, but it is soft and becomes concave when I put it on the DS series stick. It's just a matter of whether the stick holds your thumb or the thumb holds the stick. The texture itself is a wash for me - I don't like feeling the dots on the 360 stick, but it's good to know what absolute UDLR are on it since only Nintendo gates the sticks. In any case, they're both capable of fine movement and I've never had a problem with slipping off any brand's thumbstick, even Mad Catz'.
The triggers on the DS3 I'm not crazy about. I prefer the DS2 for this even though they're not analog. I can use them, but they don't feel good. It also seems that the 360 has another 50% pull distance and nice flat resistance across the range. I'll give them the triggers - Sony tried too hard to stick to the old design there.
That depends how you hold them, but it's possible. The 360 is more comfortable if you grip it full-on with the palms of your hand, for sure. I'd even say that approach borders on suicidal with the DualShocks. I really don't like doing that with any controller though - it makes hand sweat badly obvious and reduces thumb mobility to switch between pad/buttons and sticks, or greatly increases strain when I do. It's possible not to hold the 360 that way, but it seems to strongly encourage it.
You hold a 360 controller a lot like a GameCube or XBox controller. You hold a DualShock series controller like NES, SMS, SNES, TG16, Genesis or Dreamcast controller or a GB/GBA/GBA SP/GG/Nomad/WS/PSP system - resting on fingers, with open palms. I find that far more comfortable. I cringe thinking about how my thumbs would feel after doing something
with a full-grip controller (or what my score would be using the 360's d-pad and domed buttons.)
Though if you hold it like I do, it's way more comfortable to switch on DS because rather than using the tendons in my thumb to stretch over to the stick, I can just rotate my wrists a tiny bit and my thumb goes to the stick. I actually found for precision control, or even long play sessions, I can keep my thumb pretty much still and subtly twist the controller around to move the stick, which is a godsend if you have RSIs in your hands. Also not impossible on the 360, but the stiffer triggers make it harder to maintain such a loose grip.
Not quite sure how you mean the 360's inputs are equidistant and the PS3's aren't... On both, the right stick's right edge overlaps half the left button, and its top edge overlaps half the bottom button. Likewise, the PS3 d-pad and 360 left stick match their center axis to that of the buttons and their edge overlaps half the lower input (PS3 L stick, 360 d-pad.) The bottom inputs on both are the same distance apart - you can put the controllers face to face and they will line up almost perfectly. Actually, seeing this it seems MS was trying to make almost a carbon copy of the DualShocks when it comes to placement - they just swapped pad and stick like the Dreamcast and GameCube (though not the alpha XBox devkit, which is like a 6-button Dualshock / PS3 "boomerang.")