I have a theory about those scroll wheel "bumpers". We can't really tell from the patent, but what if those are to "add" more buttons to the system? What if you can press a quick switch button on the back, scroll to a button letter, and then lock that button in place and assign an action to it? This could offer 4 or 5 buttons PER bumper, or offer new playstyle experiences via "free wheeling" where the bumper(s) are not locked in place, but are used for scrolling, zooming, etc.
The new killer app could be something to help show off this new control style, where maybe you're looking through a scope to either search for things or shoot things, and you use the wheels for precision aim. You get on a certain aiming plane, and then you scroll a click or two with the left bumper to zoom in, and scroll a click or two with the right bumper to slowly move left or right. Say a stealth/spy game where you have to gather intel, or take out a target using targeting equipment or a scope or something. Another application this could have is quick adjustments or item switching in games, which they could really use with a huge variety of titles. If it sticks, I'm going to say that Zelda will use it for a few puzzles as well where you have to use the scrolling wheels to balance left and right across a log or rope, or where maybe you slide blocks or something into a panel on the left and are trying to match patterns doing the same with the right.
There are a lot of applications this COULD have, and the locking button thing would obviously be self-explanatory, but regardless, I think that Nintendo will do something completely outside of what I just thought of. These would be applications for things that I can think of, not the geniuses at Nintendo, I'm sure they have much bigger and better plans.