I play gamepad all the time, and at a level right around "pro > * > tournament" level. Hard to really put that well, but I'm almost consistently better with pads than sticks, save for XBox 360 (because most 360 d-pads suck for cardinal/diagonal orientation, and they have the same problems as thumbsticks - one degree past horizontal and you're airborne). I *can* play arcade sticks (save for Mortal Kombat) fairly well, but I get consistently better response with my gamepads. I can keyboard that shit better, too. (But then, my first gamedev project was based on the SSF2 engine. So take that with a grain of salt...)
As for Dark Souls, I cannot recommend that enough. It was my pick for GotY.
The only user here I think that's more vocal about DkS is C.A. Sinclair. The controls take a little getting used to (especially if you're used to the whole thumb-button-to-attack scheme). It's a really incredible experience that doesn't really let up and always keeps you guessing and on your toes. Plus, the game is atmosphere incarnate, the combat system is both flexible and deep (you can have plenty of options, but not all of them at once), and even many of the AIs aren't stupid about it.
The Humanity (Body/Hollow form) system is about as technically complex as it gets, and the game doesn't quite do enough to clairify the advantages and disadvantages of it. But we'll cross that bridge if/when you get there.
Certainly check it out, and don't let it bully you out of pushing through a good portion of it. It can be tough as nails if the game's unfamiliar to you (or you've never played Demon's Souls or King's Field). One final word of warning - it will probably screw with your standards of both RPGs and Metroidvanias. And probably level design of 3D games on the whole (if Sonic Generations didn't already do that).
I mean that in the GOOD way.
Oh, and if you're uncertain about buying it, Northernlion is doing a through playthrough on YouTube.
IF you decide you want to get/play this game, immediately stop watching the playthrough, and do it.
That element of surprise/exploration is key to it's full enjoyment, and the less you know going in, the more you'll love it.