Despite how UPN aired the series, Voyager really does need to be watched in a combination of both Production and Stardate order because, contrary to what people believe, it does have serialization and continuity.
Season 4 for sure! Janeway-Seven of Nine's relationship was the best plot Voyager got and this s4 offered a beautiful palette of emotions for both going from anger to anderstanding and compassion.
Voyager's strongest seasons for me are Season 4 and Season five. Its mostly Seven episodes with Janeway episodes and a few others sprinkled in. Of course the Doctor gets to shine as well. Living Witness, Prey, Timeless, Year of Hell, among others are my favorites.
Someone once said, that TNG got better when Riker grew the beard, and DS9 got better when Sisko shaved his head. Maybe Voyager got better when Janeway bobbed her hair. It's all about the makeovers, kids.
I'm going to be controversial: season one. To me it is still the best season of Voyager. The crew spar off each other, some really good sci-fi stories, some great humour. To me it and season two are the Voyager golden years, it hit the ground running. Upon a re-run I appreciated season five more than I remember, it's the better on of the later years.
I have said it many times before and I will keep saying it: give me Threshold anytime over a mediocre episode where watching the crew beating the baddies and finding the 'solution' turns out to be a tedious, formulaic affair. Threshold may have plot and logic holes larger than from earth to the DQ yes, but at least it's entertaining (and I'd say it's entertaining exactly because it is so absurd and way-out there). At the end of the day, I watch to be entertained, not to have my sense of logic and sense satisfied. And Paris even gets a tiny bit of actual character growth, as at the end he realizes that setting an incredible record isn't the quick fix for his self esteem he hoped it would be and that opinions of others about him don't matter that much in the end.
That's more character growth than you see in most episodes. Of course, turning into a lizard and... ah, seducing one's captain would be expected to have at least some effect on a person.
Especially if salamander Janeway was the one who actually wanted to get it on with salamander Paris...
The first episode of season 3, when Sudor goes midieval on the Kazon. IIRC we don't have anymore Kazon episodes after that. To me that's a big plus.
The first few seasons are the only ones where they feel like a ship lost and alone so the overall feel is better but the best standalone episodes are in the later seasons
I really liked VOY in the beginning, when there was so much potential and the first season especially really does have a sense of isolation, that they are one ship alone in the DQ. Also the fact the cast really did feel like an ensemble, the later seasons see anyone that isn't Janeway, Seven or the EMH being brushed aside. Granted they do have the Kazon, a lackluster foe, but they are redeemed with Seska leading them, whilst the Vidiians are just creepy body snatchers. Threshold is an interesting concept though the execution could've been done better. My one issue with it is the ending. After being evolved to a new stage of human development the EMH manages to revert Paris and Janeway back to their less advanced form without any effort, after effects or long-lasting issues, so why wouldn't he be able to do that with all the crew once they got to Earth after using warp ten, when they'd have all the resources of Starfleet to hand to help with the 150-ish cases of evolution?
^What about those lizard babies that were so carelessly left behind? Suppose that species evolves to sapience again and find out their origins..... lots of people have crazy creation myths, but their actual origin story would top them all ...they'd probably be the ridicule of the entire galactic population of their approximate peers in that era ... ('A species that originated after some ancestors of the omnipotent H-continuum, that weren't too much unlike ourselves, flunked a transwarp experiment, sufferent horrible mutations and decided to have sex afterward, HAHAHAH! ')
Maybe the Voth stumble across them and together they decide to exact their revenge against humanity...