The Maquis didn't fall in love with Janeway immediately. Belanna Resented having to toe the line behind Joe Carey and didn't "fall" for Janeway until the Captain started giving her a lot of 1 on 1 interaction where she demonstrated her respect for Torres' skills and intellect.
The "Maquis", in the person of Seska in season 1 and Hogan/Jonas in season 2 were not in love by any way, shape or form, with Janeway.
Seska was a Cardassian spy, she doesn't really count, considering she had no real loyalty to the Maquis. I will concede the point on Jonas, but he was willing to betray everyone, there should have been way more regular friction between Janeway and the various Maquis, those two crews coming together should have take longer and had far more growing pains.
Also by the time "Learning Curve" comes along, Torres has developed a cultish devotion to Janeway, essentially telling Dalby he had no right to question Captain Janeway. That comes off as unrealistic, that Torres would be that devoted to Janeway that quickly.
As for the EMH and Janeway, in season 2 the Captain actually did bow to the Doctor's orders to go to the holodeck and blow off steam because she was obviously burning out. (Persistane of Vision) What she did NOT do, is let the Dioctor put her on enforced leave when the entire crew of voyager consisted of 6 people and 1 hologram. When Voyager didn't even have a first officer of a pilot on board, the tactical officer was blind and there wasn't an option to call starbase 12 for replacements.
Her threatening to delete the Doctor was still way out of line and dangerous considering in that situation they would have needed a medical officer and frankly the Doctor was correct that Janeway was behaving irrationally in that situation. Picard never treated Data with that level of disrespect because he was an artificial being.
Janeway was difficult for PTB to get a handle upon, and I assume it was because she was a woman. Mulgrew herself said she went to TPTB in season 2 and told them to just write her as a Captain and let Mulgrew worry about "the woman", which they finally did.
As far as how Star Trek Captains and crews are written... let me remind people about a little film called First Contact, where Picard ignoredthe advice ofhis Tactical Officer and his Physician and looked like he was going to run off a cliff... and like the lemmings they are his crew went to follow him until a 21st century woman said "THUS IS STUPID!."
WORF: Wait! Captain, our weapons are useless. We must activate the autodestruct sequence and use the escape pods to evacuate the ship.
CRUSHER: Jean-Luc, if we destroy the ship we destroy the Borg.
PICARD: We're going to stay and fight.
WORF: Sir, we have lost the Enterprise. We should not sacrifice...
PICARD: We have not lost the Enterprise, Mister Worf. We are not going to lose the Enterprise. Not to the Borg. Not while I'm in command. You have your orders.
WORF: I must object to this course of action.
PICARD: Your objection is noted.
WORF: With all due respect, sir, ...I believe you are allowing your personal experience with the Borg to influence your judgement.
PICARD: You're afraid. You want to destroy the ship and run away. You coward.
CRUSHER (OC): Jean-Luc...
WORF: If you were any other man I would kill you where you stand.
PICARD: Get off my bridge.
LILY: So what do we do now?
CRUSHER: Carry out his orders. Dyson. Kaplan. Start working on a way to modify the weapons systems.
LILY: Wait a minute! This is stupid. If we can get off this ship and blow it up, let's do it.
CRUSHER: Once the Captain has made up his mind the discussion is over.
(Lily goes after Picard)
As Janeway would say... "A Starship is not a democracy."
The difference is Picard's actions in that movie were clearly being presented as wrong in that movie, the writers rarely present Janeway's actions in a similar negative light.
In Scorpion, Janeway made an alliance with the Borg and what came of this alliance? Janeway helped the Borg win a war where they were the agressor and this led Species 8472 to decide that the Federation was a threat to them and they nearly declared war on the Federation. Janeway almost got the Federation involved in a war with a vastly superior force, that would have crippled the Federation and no one called her out on any of this. At least someone took Picard to task when he was behaving irrationally and we were supposed to be on Lilly's side when that happened. No one ever did the same with Janeway.
How many scripts were there really that directly addressed her being a woman?
Sure, there were a ton that acknowledged that she was, indeed, female. But there was never a script where she had any kind of problems being in command because she was female. Her core personality traits seemed to me like she was impulsive and stubborn, and unwilling to compromise. And yeah, sexist jokes could probably be made based on that description (One particular poster), but none of her personality traits had anything to do with the fact that she's female. There were stories where she was actively heterosexual, but how is that a story about her being female?
Sisko had an entire story where he received a false vision where he was back in the 1940s, unable to publish his story because it was written by a black man. They never addressed sexism directly in Voyager.
Perhaps I making an assumption here, but I do think the writers neutered potential conflicts and other characters, to make Janeway look better because she was the first major female captain. Maybe I am being unfair and the Maquis story and Chakotay as a character were watered down due to imcompetent scripting, but the episodes with Janeway as a Mary Sue and the crew's cultish devotion to her makes me think otherwise.
It seems like they took the easy path, rather then the hard path. Instead of having her slowly earn the crew's respect through various feats and acts of good will, it seemed like most the crew almost instantly fell in love with her, even if it didn't make sense for some of them to do so. The level of loyalty went beyond healthy respect to slavish devotion and it didn't ring true.