They really should make mode shifts an activator option for buttons. Like, keep the original system for the trackpad/analog stick/triggers, but add in a "mode-shift" activator that lets you pick what button on the controller shifts it, and what bind it changes to.
It's kind of hard to flick, especially when you're in a pinch, but it's doable. I found raising vertical friction the trackball to max really helps stabilize flicks, especially in a shooter since you're mainly turning left and right. I started playing CS:GO because of some replies I got on that thread, and it's generally manageable to watch your back once you get used to flicking. You can also use flicks to strafe around an enemy once you get good enough! Though again, I'll admit it's hard to get down, it's definitely worth learning with the limited space you have on the pad.
Change your dead zone size and rest your thumbs. It will change your life.
Ooh, this game. I've slowly been playing through it with the Steam Controller (currently halfway through Swamp), and I've found it a great way to learn the trackpad. What really helps is that targets are so big. Probably a little easier with a mouse, but the awesome part is that it's feasible. I've completely avoided the auto-aim feature they threw in for gamepads, and have been going through it just fine. Granted, retries are common as I try to three-star levels, but I'm sure that's unavoidable on your first playthrough either way.
Bending my thumb has never been a problem. How much are you bending it? Maybe loosen up your angle a little. Also, if it's taking too much effort to move your thumb, consider disabling smoothing. It makes adjustments require much more movement, among other things. Then if jitter becomes an issue, just lower the trackpad sensitivity and raise in-game sensitivity in steps until it's stable.
Anti-deadzone is great for games with full analog movement, but I really recommend using directional pad mode with the joystick for 2D stuff like Freedom Planet, with haptics to high and a big deadzone (75%). When you hit the input, you can tell through haptics in a similar way to a d-pad, which helps a ton with quick adjustments. Much better than regular joystick implementation in 2D games.
I get this sometimes as well. Sadly, can't speak for the new beta patch that was just released, though I hope it fixes it. (EDIT: Nope, still happens. Overlay and Steam crashed altogether while I was editing stuff, actually. Haha.)
This is still my largest surprise with the controller. I was a bit unsure because of its size and my relatively small hands, but since you hold it completely differently from other controllers it actually turned out to be the most comfortable for me.
How are you holding the controller? And how big are your hands?
The best thing to do is to just ask for help around the community based on what's troubling you. There's no real unanimous opinion on each part of the device, so a lot of good tips end up spread across people. There are plenty of generally well received controller guides on Youtube, but none I'd say are cohesive, since everyone has a different experience with the device. Though it's still worth watching through them, since you should find settings that work for you eventually.
The key binding interface has issues with mouse from my experience, try manually selecting it with the left stick and the a button.
At least disable pointer precision. Acceleration is going to knock off your aim in shooters, so it's best to disable it on all ends. I've been having a better time without it, honestly.
I didn't mind the paddles, but yes, the triggers are absolutely lacking, and the click at the end is too light. Hopefully this is fixed in the revision, because I rarely use soft pulls for this reason. The GC controller did it perfectly.