It's all in the presence. Bujold's Janeway is very clearly a scientist first, captain second. Now, that might fly if Voyager had been a series about a science ship exploring the unknown phenomena of the Alpha Quadrant, but for the Voyager we got, we needed a CAPTAIN. Bujold played her quiet, and if we'd had her for seven years, Janeway would not be the popular character she is.
Admittedly, given how it might have given a chance for the characters who were shafted in development in the Voyager we got, I'm interested in what might have come out of seeing her as Captain Janeway full time, but I definitely consider Mulgrew better in the roll, and am glad that we got Kate instead.