I find even considering these rumor to be very insulting towards Nintendo.
I think a lot of people refuse to believe the rumors just because they don't want them to be true, not necessarily because they don't think its possible.
Not wanting it to be true isn't the reason, it because they're ridiculously bad. Oh look, there's a new rumor from 01net that states Miyamoto is really a secret Nazi-Communist-Werewolf foreigner that's trying to destroy America. But hey, that might be a good thing. He's now more motivated to make more addicting games so kids grow up as weak nerd that don't join the US army and/or Vampires ranks....
There's no room for a 2nd stick add on, no good way to power it, no good way to connect it, no way to grip it, no use for it in a VAST majority of games, the few games the could use it are much better served by gyros and touch. There is no way in hell ANY Nintendo engineer would be going "OH ****, WE FORGOT A SECOND STICK! OUR SPECS ARE NOW INFERIOR! WE NEED TOP OF THE LINE HARDWARE AT ALL COST!!!!1111one" and staying up all night trying to correct it. Nintendo has never been in a rush to upgrade their existing hardware with add on to boost their feature set. The GBA/3D were held back for years, Nintendo Playstation and N64DD were canned before release. Wiimote+ wasn't released for years after and that probably was to easy the transition pains to the WiiU. This rumor is clearly the mindset of a sony fanboy (The only accurate rumor they had was for the psVita; the wiiPad ones were repacked wiimote rumor). Why are people giving these rumors the time of day?
I agree it would be awkward, and that would be a strong incentive to get people to upgrade to the newer model (which is good for Nintendo because it means more system sales).
It would be a strong incentive to abandon Nintendo and to drive them into bankruptcy. The last thing they want to do is take more risk and increase people's jitters of rapid system hardware updates...