I played 50 minutes of System Shock 2 just now on my TV. It's late, and I didn't feel like editing ini files, so I left it at a low resolution.
The game ran fine. I spent most of the time going through all the tutorials and slowly editing the default controller layout. Switching between the use mode and the first person mode felt fine (I bound it to select.) I got everything working, and began playing. I died in the first sequence where you have to fight people, but I felt kind of scared and immersed in the game like I never have before. I forgot to keep track of my health, but I was really enjoying myself. I'm excited to keep playing in the coming days. This is the best I've felt about the final version since I got mine a few days ago.
I made my System Shock 2 configuration public, as 'Trial By Game' if anyone else wants a starting point.
As a side note, I made a point of trying to avoid the 'mode shifting' features of the controller layout. I'm curious about other people's opinions, but I think that I am going to try and keep my layouts as close to the defaults as possible for now. They seem reasonable and intuitive. I suspect they will be how a lot of people interact with the controller -- the defaults will probably work well for many games. If that's the case, when someone comes to a game like System Shock, which does have some significant differences from a modern FPS, I'd like them to feel comfortable selecting my configuration. There will be a few differences, but they should feel comfortable glancing at the description and getting a sense for what to do.
To tie this back to 'mode shifting,' it requires you to drift from the defaults, and actually remove some. I suspect using the Grips to mode-shift will become a common method, and if so, it would require changing the placement of Crouch (Left Grip) or Reload (Right Grip). For first person shooters, we currently have Bumpers, Grips, Start/Select, left pad, and right buttons to work with. That's at least 14 buttons. It shouldn't be much of an issue.
Even for RTS games, I suspect I'll shy away from using the 'mode shifting' feature unless I see a very strong need. In each RTS, the mode shifting will be doing something completely different, and that will have problems down the line. I might create a layout that works great for me playing a particular game. If I stop playing that game to play something else, I suspect I'd forget the old controls fairly quickly. I'm not sure I'm too excited about having to use the current UI to figure out what each mode is and how it works every time I want to pick up a new game.
I suspect we'll need to come up with some sensible defaults for various genres. As a very basic example, MOBAs and RTS games will need a common way of attack-moving. Making sure defaults are sensible for each genre is something that I've been thinking about for a while now. The better the default setup for a genre is, the lower the cost of switching games with the controller will become.
Edit: I feel like I'm taking this all a bit too seriously, or overthinking it. I probably am. If so, apologies for the wall of text.