But Junior WAS the de facto boss in Season 1. He had full power, Tony was just the one the capos went to complain to. The whole "official boss/front boss" arrangement with Tony started after Junior got arrested, and Tony took over his operations and ran him out of business, leaving him with just 5% of everything. The entire point of why Tony didn't want to be boss right away is so that Feds concentrate on Junior instead of him, even after Junior was in custody - it's better if the Feds think they have the Boss himself and not just a capo, though that didn't exactly work out as they quickly found out that Tony is the front boss.