Make her interesting, but not completely central. Science was Data's. He just knew diplomacy and what direction to go. Janeway pretty much does everyone's job, going so far as to supply Tuvok with security advice or Torres with solutions to ship troubles. That kind of perfection turns viewers against a character.
Flaws are critical.
Benjamin Sisko was bold, but lacked the diplomacy of Picard. Kirk lacked diplomacy at all, but had double the boldness. Of them, only Sisko knew a bolt from a plasma coil. Paramount has few options. They could kill her off and replace her with Chakotay, but politically their hands may be tied behind their backs, given the interviews he gives and what he says about them.