I think by 'Choose Your Story' users tend to take the phrase literally, meaning second person adventures are the norm...however, an interactive story's x factor is giving the reader the ability to dictate the crucial choices of the story protagonist. It adds an extra dimension to the potential immersion because the reader feels like they have semi-control over this constructed world.
Anyways. my point is that the protagonist doesn't have to be the reader 'i.e second person', I actually prefer third person because it has a novelistic, narrative tone overall. Either way if you can write well, you shouldn't worry about which perspective you use, because i don't think anyone reading is gonna crucify the creative decision, or take a massive dump on you in the review section.