Now that it exists, though, I think we'll see more and more games use the CPP. I'd almost guarantee that most of Nintendo's first party titles (i.e. the already announced Luigi's Mansion 2) will use it in some capacity.
As someone pointed out, it's also currently an accessory. They've been smart so far and haven't fractured the userbase by requiring it for any game. I will say, however, that I'd be shocked to find someone who has used it and DOESN'T want it incorporated into a redesign somehow. Just from my own experience, I find RE:R to be perfectly playable without the CPP, but I'd never go back to that after playing it with a second stick. I think the difference with MGS3D will be even more pronounced, since I gather that it plays rather like Splinter Cell 3D without the CPP... which, if you've played SP3D, you'd agree is very far from a

ing good thing.
My view is this... it will be in a redesign. Period. Why? If they don't, they'll need to create an ENTIRELY NEW CPP accessory for the redesigned system, which seems like a gigantically stupid measure to take when they could simply toss a second stick into a new 3DS. The second stick is out there now, so it's not going away. I'd be foolish not to just add it to a new system.
In terms of a timeframe, and I'll admit to just pulling this out of my ass, I'd say we have at least a year before a new version of the system is out. My thinking is this: if it were this Spring, we'd know about it already. Same with summer (at least some concrete rumblings, anyway). Nintendo has already announced the WiiU for Fall 2012, and it makes no sense to launch a new 3DS at the same time. Spring 2013 will mark 2 years since the 3DS launch, which I think anyone would agree is a decently acceptable timeline for a new version. Not too short to make early adopters angry, and not long enough to kill interest. That's just my take on it.
Oh, and just on another topic... having spent a few hours with RE:R in the same week that I spent time at GameStop with Uncharted Vita, I can safely say that I'm not quite as impressed with the Vita anymore. It's nice, but RE has shown me that it's definitely possible to create what most people would call a 'real' (graphically, gameplay, etc) game on the 3DS. Easily the most impressive looking 3DS game to date.