Firstly, it's nice to enter into a civilised discussion on this topic !
You are right that it was about time there was a female Captain in Trek if gender bias is truly be a thing of the past by, er, the future ! There have been strong independant female characters in pre Voyager Trek - I am particularly fond of Kira, but even if higher in rank (i.e. Admiral Nechayev) they were never 'in charge' on the show, i.e. the Captain...
I would have delighted if Janeway had been written better in a better show - I can't really move past the lack of quality and care in the making of Voyager. The lack of character development, silliness with power rationing yet use of the holodeck, infinite replacement of torpedo's and shuttles, battle damage disappearing, acceptance of Maquis crew, Maquis / Equinox crew that were never seen again etc. etc. all kill Voyager for me. In addition, Kate Mulgrews mumsy Hepburn thing just grates on me (yes, she may be a very nice person and could just happen to speak like that) but that's my take.
As I see it, Janeway did women a disservice - it was time for a great female lead character, and she wasn't it...
Likewise on the civilized discussion front.
I agree Voyager had its share of issues (all Trek series do). Many fans have jokes and theories about the endless supply of shuttle crafts.
For all it's faults, I still love it and Janeway. Could she have been better? Of course! But, I think what sold me on her was her compassion and never wavering from her principles. (Kate Mulgrew has even joked and agreed with fans that the writers made Janeway seem like she was bipolar by her contradictory actions).
Like you said, of course females always had a presence in Trek and Janeway wasn't even the first female captain, but the first true female leader we had.