Re: Finished season 3 on DVD - scratching my head at the Voyager hate.
^ Yup, season 4. I've been looking forward to Year of Hell all month (despite the bloody great reset button of doom)!
After just finishing season 3 in the last week or so, I'm not sure it is as good as I remember... there were some shockers in there - Remember, Rise, Displaced come to mind.
I think season 2 was possibly their best season with a view to the series as a whole - it had recurring and evolving plotlines (through Seska, Jonas and the Kazon), and seemed to have a stronger continuity between episodes than later seasons.
For individual episodes, seasons 4 and 5 have the majority of standout stories I think. At the time, I think Brannon Braga did wonders for the show when he took the reins in season 5. Equinox is without a doubt one of the strongest episodes of the series (that doesn't rely on any reset buttons!).
Seasons 6 and 7 are pretty poor I think. I didn't realise it at the time, I just thought "meh, that's not so bad... should be some big explosions next week though...". Instead there were some pretty infuriating stories. Survival Instinct for instance - THERE'S A BAJORAN IN THE DELTA QUADRANT, WHY DON'T YOU THINK THAT'S ODD?!
Fair Haven and Spirit Folk were just "ugh". I didn't like Muse or Tsunkatse and I've never really been sure what The Haunting of Deck Twelve was actually about - pink smoke as I recall. Unimatrix Zero marked the point for me I'd officially had enough of the Borg (being 16 at the time, this was a very mature opinion for me to make

).
Season 7 was just shots in the dark at stories... we had at least 4 stories about holographic rights or other jiggery pokery involving the Doctor, two about Seven's "development", Workforce (which lent nothing to the series and didn't need a two-parter), and then you have Endgame. Also, I felt Ethan Phillips got
really short shrift all season. In its defence, you have The Void.
As someone's said above, the characterisation wasn't consistent, there were too many stories that just didn't work, or were kind of pointless, too many themes were done to death. The thing I enjoyed the least was characters being sidelined just to keep up the Janeway/Seven/EMH dynamic.
After Equinox part II, I think the show very,
very quickly loses its way, and I think that's where a lot of the hate comes from.