It would have been a lot more interesting if the Voyager crew had to work with an actual enemy.
Here's what I'd have done, had I been in charge of
Voyager.
Season 1 takes place entirely in the Alpha Quadrant. Janeway and her ship is assigned to flush out Maquis cells in the Badlands. That's the overarching plot, though there's still room for
TNG-ish "strange new worlds" adventures in the Alpha Quadrant.
The "big bad" for the first season is the mysterious Chakotay. And we see Chakotay do some
seriously bad things. Perhaps there's even an episode that shows us the conflict from Chakotay's perspective. At the time, reviewers would say "Oh, this is
Star Trek being edgy, doing an all-'bad guys' episode."
Then, "Caretaker" is the season 1 cliffhanger. Half of the main cast is killed, like Janeway's first officer, medical officer, etc.
You expect that in the season 2 opener, Janeway is going to pull a rabbit out of the hat, return to the Alpha Quadrant, and capture Chakotay. Only, it doesn't happen that way, and the ship is stranded in the Delta Quadrant.
Some characters that fans had grown to know and love are dead. Some characters fans had accepted as villains are now, if not heroes, then reluctant allies. And we'd have some idea of Chakotay as a leader.
Instead, Chakotay was basically fiated as a leader, and he was never developed enough afterwards for it to work.