Yeah, I gotta agree Janeway stepping up as the inexperienced first officer would've been way more dramatic. Really in my opinion they did her and the story a disservice by having her be... by her own words... "larger than life." They made her have to be so absolute in her authority, and make sure the audience knows it, that they had to manufacture dilemma's and have her "make the call" to resolve them time after time. As if making her decisive and authoritative would somehow compensate for her being female. Unfortunately all this really did was make her look silly at best and downright insane sometimes. She would've seemed far more human and sympathetic if she showed signs of weakness and doubt more often. Instead of just seemingly making the call without even thinking things over half the time.
I also definitely agree that the Maquis were an underused element. This was supposed to be part of the premise of the show, a divided crew having to work together despite it all to get home. Yet the number of episodes where the Maquis are a major factor is a single digit number. Heck a couple of them are holodeck/distorted reality episodes. Really by season 2 they were just all frankly assimilated into Starfleet. Personally if I was one of the Maquis, I'd be rather resentful that I was pretty much conscripted into a military I don't care for and my captain blatantly states on numerous occasions she's willing to sacrifice my life for values I don't believe in.
As for the Cardassian officer bit? Heck... all they'd have to do with that is not make Seska join the Kazon, but get found out anyways. That would've been way more interesting and dramatic than just having her become another generic bad guy(though I suppose the evil impregnating herself with Chakotay's kid was original... and bizarre). I think Star Trek's always been way too human(way too western) centralized. If there's supposed to be this big galaxy with the good guys being a multiraced Federation... why are 75% of everyone humans? Having Seska around as an experienced officer would be interesting. She'd bring another viewpoint to the table, and create tension and drama with both the Starfleet and Maquis people not trusting her.