"One thing I'd personally like to avoid doing is elevating supporting characters to a sort of main cast role."

Is that strictly for you, or are you trying to tell everyone else not to have their characters be of some importance as this goes on? No one's going to be the level of 'special' that Naruto and Sasuke are because 'loljinchuuriki' and 'lollastoftheuchiha', but it sounds like you just want those two to take the lead in everything. I hope I'm wrong, because if that's the case there's almost no point doing this if we're all still going to be second to those two characters when it comes to plotlines.