There are pros and cons to including the right circle pad. 3rd parties could have held their games hostage or threatened to move development to Vita if they really wanted to force Nintendo's hand. Nintendo, in turn, could have made it a prerequisite that all games have a single circle pad option. There are a number of ways this could have played out that could have had positive and negative effects on consumers.
Ultimately, I don't believe this will affect 3DS in the long run. It's still a viable platform. Sony released 3 revisions to PSP and never added a second analog nub. That wasn't the reason DS dominated it. And Sony actually doubled the RAM which could have affected performance. People didn't really kick up a fuss about that. If I was a 1000 model owner, that would have irked me.
Like most things, I think people will generally forget about this after a while. Many games play just fine without it. I always go back to God of War: Chains of Olympus. It was extremely faithful despite less functionality. Most developers will make good games regardless. So far, they have.