Though personally, it's close between the special and manga since those actually felt like they were all part of the same over all theme and events in the games. The anime (like most anime who's episodes are at least in triple digit count) just felt like filler and fan service most of the time instead of moving the story along and getting to the next point of interest.
You do know that there's several main characters out there now, right? Each time either a new set (Ex:R&B,) or a new third game, (Ex:Yellow,) is released, a new arc is made, with new characters to go with it, though some of the older characters, (Red included,) stick around as well. And it's still going on today. Also, the more common name for it is 'Pokemon Special.'
I know all that, but even if protagonist might have been the better word to use (and Red certainly gets more panel time than Blue or Green) that hardly undermines the general point I made. Also, while Special might be the name in Japan, in English-speaking territories it goes by Adventures.
I don't just mean Blue or Green. Yellow, Silver, Gold, Diamond, Pearl, Black, White, etc...