I would like DualShock controllers better if it weren't for the fat & stubby "handles"... regardless of anything else, I've always found it to be the most uncomfortable standard controller of any home console in the last 10 or so years due to said "handles". It looks like this may have finally changed a bit on the PS4 (slightly longer and slightly more ergonomic handles! FINALLY!), so I'm extremely interested in physically trying the controller out.
In terms of raw physical ergonomics (in no particular order), I've found the GameCube, 360, Xbox Duke, and wiimote + nunchuck to be the most comfortable (haven't tried any Wii U controllers yet). However, none of those controllers have a SNES-style dpad & button arrangement which makes them considerably less flexible in their universal-game-playing functionality. Therefore I find the Classic Controller Pro to be the next best thing, though its ergonomics are somewhat less comfortable with its N64-esque handles. (people compare the CCpro to the dualshock, but physically it feels much more like an N64 controller without the middle prong)
Funny thing about the Xbox Duke - I have small hands yet I find the Duke much more comfortable than the Xbox S controller. The underside/backside of triggers on the S end up hitting against my middle fingers. My theory is that my small hands may require me to "choke-up" on the controller for my index fingers to rest flat on the triggers, which in turn makes the rest of my hand move forward/upward resulting in my middle fingers bumping into the underside/backside of the triggers.
