I see I missed a spirited debate, and in the interest of peace on earth, and good will towards men, I shouldn't revive it in any way, but I do have a few comments.
John is right that Janeway and Picard are two different types of Captain. Picard sits on the bridge of the flag ship of the fleet, with the very best of every type of officer and crew that a captain could hope to have. Not "just" the very best, but a multitude of the very best. IIRC, a Galaxy class starship has a crew complement of 1000, Kirk's old constitution ship had 400, while Janeway's Intrepid class ship had 150. Picard's ship frequently took on and let off old crew, just look at the disappearing reappearing acts pulled by Dr Crusher and Acting Ensign Wesley, and it frequently put into various starbases for fuel and recreation, not to mention educational or diplomatic conferences. Being different doesn't mean one is bad and one is good, just that they are different.
John makes several pleas for Janeway to consider other alternatives to the brute force that she frequently used... "I was taught in the Academy that flying a starship is a delicate thing, but one thing Ive learned, over the years, is that sometimes you just have to PUNCH your way through." Statements like that certainly seem to bolster his argument, and yet I always give her "leeway" in these grandiose statements because sometimes there isn't "time" to be delicate, as the second ep in season 1 demonstrated. In "Parallax" Janeway and B'Elanna have worked together to reason a solution to being caught in the event horizon of the quantum 4 singulariy, and despite putting their plan into practice the "hole" they created wasn't big enough. Every second they delayed, the hole got even smaller, so the delicate woman did what any hulking male Captain would have done in the circumstance. She punched her way through.
Our Moderator reminded us that the Captain risked herself to "pull a switch" in season 3's "Future's End", an act that not just saved her crew from living out the rest of their lives in the 20th century, it killed the man who would rather threaten 29th century Earth with destruction, than miss out on the next "killer ap" for his computer company. There was NO time for diplomacy or science, it was kill or be killed, and the Military Officer, not the scientist made that decision. In case John was recalling the time she ran through flames in "Year of Hell"... again that was a do or the ship dies" thing... no time to send in the reserves since they didn't have any reserves.
I hate to admit it, but so many of the examples that John has picked are from my favorite eps, like "Scientific Method". The aliens have already nearly killed B'Elanna, and have tortured everyone on the crew, including the Captain. They try to reassure her that the death rate from their experiments will only be (not sure here) 30-40% of her crew, and that she should just sit back and accept it. She won't be able to stop them all before they kill again, and just for spite(?) or because her experiment reached its conclusion, an unknown ensign falls dead at Janeway's feet. Janeway can't take it, she tries to bring the young woman back by doing that ancient of all rescue methods CPR even after the Doctor gives up... but it doesn't work. It wasn't one of "her close family" that pushes her over the edge, its this nameless woman who did no one any harm that pushes Janeway to the realization that its NOW or NEVER. We ALL die or we all live by ridding ourselves of this alien research team immediately. How best to do this? Scare them off the ship once and for all ! And by gosh it worked. "I never realized you thought me reckless, Tuvok." "Clearly, it was an understatement, Captain." :-)
Speaking of favorite lines, if not necessarily in favorite episodes, I recall Janeway asking her Bridge crew why they couldn't do "technobabble" to capture the wormhole in "False Profits", and Kim basically tells her beause they'll blow up and she responds, "Then I guess we won't do that." She does listen when she has to. Just like when she invaded Tuvok's personal space in "Meld". He told her not to enter his room, and she entered. He said don't come closer, and she did. He told her NO further... and she stopped. She could judge just how far she could push her relationships, before she could push no more.
Tuvok is a special case, and there's nothing logcial about their friendship, but it exists so we have to accept it. But even this friend, who she trusts implicitly, never got promoted until 5 years into their Delta Quadrant mission. In fact, the Vulcan is the only one who got promoted, if you don't count the demotion/promotion of Tom Paris. I don't count Chakotay, he just "transfered" from his ship to her's with a best position she could offer. I also don't count B'Elanna as a promotion, since she was Chak's Chief Engineer and simply was assigned to same once Janeway realized she had potential to be a good officer. And I also don't "count" Seven, since it was Seven who (with Harry's help) designed and actually built the Astrometrics lab. I'm pretty sure Harry wouldn't have wanted to give up his post as a bridge officer to hide away in the Astrometrics lab for the rest of the journey.
Being part of Janeway's "family" was also no free pass on Voyager, as Tuvok would be the first to explain, just recall the dressing down he received in season 1's "Prime Factors", or as Tom would tell you after his 30 days in the brig, or as Harry would tell you after he consorted repeatedly and against orders with a female from a xenophobic race.
But to get back to the "Good Shepherd", although I think its silly to see Janeway get lost on deck 15... (Heck, there's ONLY 15 decks, you'd think she'd walk them daily just for exercise.) I think its totally believable that she isn't "so" involved in every one of the 150 lives under her command and that she didn't realize these 3 had slipped through the cracks. Chakotay is in charge of personnel, and the dept heads are in charge of their own people and report to him. I did think it amazing that the Captain quickly saw that these three had never been on an away mission, and that in order for them to feel like a part of the Voyager team, they had to go on one. It made me think of the conversation between Janeway and Tuvok during "Juggernaut" when Chakotay became disabled and B'Elanna took over the leadership of the team. Tuvok asked if he should go to the tanker and assume control, and Janeway said "No." Sending Tuvok would send B'Elanna the wrong message, that she didn't trust the troubled Engineer, and she did trust her. Sending those three on a mission with Harry, or Tom, or even Chakotay would also be sending those three misfts a message, that the Captain didn't trust HER life with their questionable skills. Janeway also realized, that after 6+ years of trusting these three young crew to their dept heads, that the Captain HAD to get involved because, in the end the Captain is responsible for everything.
After all, in the end, she ISN'T a scientist. She's the Captain. Its her responsibility to get these people and this ship home, and in the end that exactly what she did. In fact, she did it sixty-three years early, thank-you Captain Janeway.