Way I see it, if it were 100% popularity, Vincent would have won...BUT Crono won, so there is hope for it. And even then I never went by popularity, I've always gone by who is the most heroic or most villainous most well developed character of all.
And also, it can help because I know tons of people who when they see their favorite character get beaten by someone else they're all angry why and begin researching the winner to see "just what's so special about them" and sometimes they actually like their discoveries. yet to happen with Crono, but Crono hasn't beaten anyone my friends enjoy...YET.
Now it serves more purpose and I care somewhat cause Crono has a game coming up, and it might get him recognized even more since I've noticed whoever wins they'll usually make more of a deal for on Gamespot, where it isn't about popularity.