I know many fans were down on ST:ENT on season 1 - 2, and many didn't like the long Xindi arc of season 3. My take on that was seasons 1 - 2 had some weak episodes here and there - however the same can be said of TOS, TNG, Voy, DS9.
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I've given some thought as to why this series is so special to me and have decided it's at least partly because of the time it was produced. I had just purchased my first house and moved in with my wife of 9 years (at the time). In a nearly empty living room with only a TV and a card table (we were waiting for furniture to arrive) we watched Broken Bow. The theme song spoke to us and we identified with it.
That is a lovely story which almost makes me like the theme song!

Re the low reputation of the first two seasons, and what IrishNero was saying about the Xindi arc, I've found my rewatch of the series very interesting for the way I reassessed some episodes. For one thing, I think we tend to evaluate things according to our mood at the time, so if we're tired or irritable an episode can seem worse. OTOH I find that if I've just watched a great episode, the next episode gets a little boost from that.
One thing about season 4 that surprised me was that Bound is a better episode on rewatch. When I first saw it I disliked what I saw as a very sleazy atmosphere, capturing the worst of TOS in that sense. But when I watched it again, and was aware of what was really happening in the first part of the episode, I enjoyed it more and found it more interesting.
Has anyone else had that reaction?