There are some that are... acceptable. But you're right.
The fact that Apple has announced APIs for game controllers on iOS means that this will change with iOS 7, and that could be a big problem for Nintendo.
That seems to be a de-facto-standard away from being solved though. Someone, or some collection of someones, are going to hit on a controller and/or case and/or variant device that establishes some set of inputs that clicks with the market. [1]
And developers will design for said standard and that will be that.
That seems much easier (if not entirely inevitable) than Nintendo discovering some way to halt and/or reverse the trend away from dedicated gaming devices.
[1] a standard along the lines of the modern console: "dual analog sticks, d-pad, shoulder buttons, four face buttons"; or stand-up arcade fighter's: "analog stick + 6 buttons", etc. It doesn't have to be one-true-piece of hardware, just a general arrangement of inputs that developers can design for.
I don't think lack of hardware or standards here is the issue. It's still an open question as to whether those same people who buy mobile games would walk around with a controller+phone in their pocket/purse.
The question isn't whether happy touch-gamers would buy these controller cases in bulk. The question is: should these cases exist and get developer support, how many 3DS and Vita gamers would continue paying a premium for their dedicated devices and software libraries?
Android and iOS already "have" the larger slice of the market. (The "touch gaming" slice) My point is that they're a very short step away from essentially taking "all" of it. (Not literally all -- focused devices may still live on -- but enough that Sony and Nintendo's current model can't sustain itself.)
Also, I think you're "off" on the size estimate.
Extend a hypothetical mobi-style battery case an inch-and-a-half on the 'head' and 'chin' of an iPhone. D-pad on the left, some buttons on the right -- maybe even shoulder buttons if you're feeling saucy.
The result is still pocketable and smaller than a Vita or 3DS. (Similarly for any number of popular Android phones -- though phones with 5" screens would push the arrangement directly into Vita-ish dimensions.)
Stand-alone controllers are an important part, but they'd be something that provides consistency on the TV-screen side, with things like GameStick, Ouya and/or Apple's rumored AppleTV gamepad play.
The fact that Apple has announced APIs for game controllers on iOS means that this will change with iOS 7, and that could be a big problem for Nintendo.