Simply put, Kathryn Janeway is heart and soul of Voyager....and perhaps even of Star Trek itself.
Scientist, explorer, diplomat, pragmatist. She always flexed her intellectual muscles at every opportunity. She would assist science officers and scientific endeavors frequently, giving her a rather hands-on approach to many missions and conundrums. Janeway had an almost insatiable curiosity in the finest traditions of Federation explorers.
And ONLY Captain Kathryn Janeway could combine a StarFleet and Maquis crew, forge alliances with The Borg, have easy going relations with Q, assuage the fears of Species 8472 (In The Flesh is one of my favorite Voyager episodes), liberate a Borg drone and make her a valuable member of the crew, and, of course, get her crew home from a potentially decades long journey from the Delta Quadrant back to the Alpha Quadrant.
Kate Mulgrew portrayed Janeway with such subtlety and restraint of emotions that would've overwhelmed a lesser character. One of my alltime favorite scenes in Voyager (and again, in the whole of Star Trek) is the scene where she confronts Tuvok after he led a disobient mission to acquire technology that could allow Voyager to get home much sooner than plain old warp drive would allow. In that scene, you could see that Kathryn was just on the cusp of crying, she was so distraught at Tuvok's disobedience. Mulgrew played it right to the cuff, and basically let the audience feel the emotion that Janeway so wanted to express.
I loved how she actually managed to get along with Q. A couple of episodes ended with Janeway and Q sharing a laugh of sorts. When Q presented his baby to Janeway, and showed his nurturing side, and the look of approval and the smile on Janeway's face....sublime.
Janeway bore pressures upon her that would've emotionally and perhaps mentally crushed a less resolute being. It is one thing for the captain of a starship to of course be concerned for the welfare and safety of his/her crew....but Janeway had to bear that responsibility a hundred fold, for they were tens of thousands of light years from home....decades away at the best warp speeds Voyager could manage. If she lost a crew member out in the Delta Quadrant, there were no StarFleet facilities from which to recruit new personnel.
The growing friendship between Janeway and Chakotay was vital to her effectiveness as a starship commander. With the wisdom of Tuvok at one side, and the sensitivities and sensibilities of Chakotay on the other, there was little that Janeway could not accomplish.
Janeway had this knack of being able to make a crewmember regret a bad move without having to resort to emphatic dressing down. Her disappointment alone was often enough to sway a wayward crewman back to straightening up and flying right.
She still tried to live up to the spirit and dictates of The Prime Directive, even though they were far from StarFleet Command and The Federation. Ultimately, the decisions to violate the PD were difficult, but once she committed to a course of action, she saw it through unless a better solution presented itself.
Kathryn Janeway, to me, represents the finest of StarFleet's officer corps, and among the finest of humanity.