I hadn't seen BSG when it was airing first-run, so my viewing experience of it was different. I watched it all in a much shorter period of time after hearing things about how great and ground-breaking it was. So here are some of my observations after completing the series.
1. The story was what kept me interested, because the characters did not. I have seldom encountered a TV show with so many unlikeable characters. By the end of the series, the only characters I still liked were either peripheral guest-characters(Dr. Cottle, Romo Lampkin) or dead.(Dualla, Cally, Billy, Gaeta) Adama is a tyrant, as is Laura Roslyn. Baltar is a slimy, self-centered traitor, most of the rest are bland or forgettable. Wait, I guess Saul Tigh was still pretty cool. Which brings me to my next point...
2. Starbuck. Ugh. Worst character on the show. Fingernails-on-chalkboard annoying. An abrasive, obnoxious, bitch with a massive chip on her shoulder and a sense of grievance and entitlement. The idea that someone like her would last five minutes in any organization that is even remotely military in style is laughable. What's worse is the obvious love that the writers had for her, so she was so often front and center.
3. Lack of humor. I get that the show was going for gritty and dark. But BSG probably had the least amount of humor of almost any show I'd ever seen. Even when the series was drawing me in with the stories, the almost total seriousness of the show made it almost a chore to watch sometimes. Sitting down to watch it, I knew I was in for forty-five minutes of no jokes, no light moments, etc. Dark and gritty is one thing, revelling in misery as you beat the audience over the head with how sober and serious you are is another. Whedon is an example of a writer who can combine dark themes and shows with tons of humor.
4. The unrealism of a "realistic" show. So RM set out to make BSG realistic sci-fi. Well, the way characters acted in a supposed military setting undermined that. Characters routinely turning guns on one another, and then the next week it's forgotten. Fights breaking out all the time. I found the actions of the various characters to routinely come out of left field.
5. It's a different show by late season 3. I've seen this point brought up a lot about the show. BSG goes from being a show about the survivors of Humanity making their way to Earth and fighting the Cylons to being dominated by angels, prophecies, and gods. You can really see the parallels to DS9 here, where the "Prophets" and Sisko as emissary arc became increasingly prominent whereas early DS9 was more politics-driven. Your mileage may vary on whether these elements made BSG a better show or not.
6. Adama and Roslyn-so Roslyn is appointed president twice, never elected, in fact losing the only election she ever fought after trying to rig it. Tom Zarek who was elected to a position, is ignored by Adama as is the quorum, while Adama carries out a totally inappropriate relationship with Roslyn that makes it seem that the civilians are being governed by a lovers' coup. To make it more absurd, Lee Adama, Bill's son, is appointed later. So... the civilians are being governed by a triumvirate of a military dictator, his girlfriend, and his son. And... we're supposed to side with them when Zarek gets frustrated with this state of affairs? It's a good thing they had to make Zarek a bloodthirsty thug otherwise fans might start to wonder...
We also got Adama threatening to shoot strikers and their families rather than negotiating with them, after he was so disturbed by Admiral Cain's dictatorial tendencies in season 2. By the end of the series, I really couldn't stand Adama or Roslyn.
7. Cylons-so... by the end of the series, what's the difference between a Cylon skin-job and a Human? Medically, psychologically, there doesn't seem to be one. They act, talk, walk, and have sex like Humans. The only difference seems to be that they can "resurrect," but I thought it odd that they made them virtually indistinguishable from Humans, yet tried to act like they were different, like how "extraordinary" it was to have hybrids. Why? Cottle seems to be able to treat them medically just like Humans.
8. The story-as I wrote, the story kept me coming back. It was clever the way they kept bringing up mysteries to solve to bring you in-where is Earth? Who are the Final Five? Who is the Final Cylon, etc. Even when I dislike or was neutral about the characters, I thought the overall story was good. Until...
9. The resolution. It's interesting to compare this show's mythology and story arc to a show like Babylon 5. You can tell that B5 had its story mostly mapped out and that BSG didn't. Because many dangling threads of BSG were red herrings or dropped completely. Hera's destiny? To be a one-line joker 150,000 years later. The Opera House vision? Meaningless. Kara Thrace? An unexplained mystery. The Cylon Plan alluded to for years? Also meaningless. Turns out "God did it" is the answer to most of the story issues, and that the characters were puppets being led to one point so Kara Thrace could make that jump. The "cycles" idea of repeated conflict was an interesting one, but the "shaggy God" story of the BSG crew as Adams and Eves was cliched rather than clever. The series finale was a big disappointment.
10. Lack of re-watchability factor. The lack of humor, unlikeable characters, intense serialization of storylines, and the nature of the series relying so much on "mysteries" means that it doesn't have a high rewatchability factor to me. The storylines were very good, and it kept me interested, but I would never buy this series in any format, because once you've seen how the mythology and story does(and doesn't) resolve, there's not a lot of enjoyment to get over it.
Many of these points seem negative, but I don't want to give the impression that I didn't think it was a good series. This is an example of a show or movie that I can say was "good" and "well-written" but that I didn't really ENJOY watching. It's a dark, depressing show filled with unlikeable characters doing nasty things, and there's very little comic relief. That, as I wrote before, makes it somewhat of a chore to watch. I got through it, I'm glad I saw it, it's thought-provoking and clever, with many good plots and storylines, but I don't think it's likely that I'll watch it again. I enjoy sci-fi/fantasy shows like Star Trek, Buffy/Angel B5, Doctor Who, etc. far more, because as I've written, they're funnier, have more likeable characters to root for, and aren't as dependent on grand mystery mythology to draw you in.
BSG was like a mystery novel to me where I just had to keep going to find out "whodunnit," but was disappointed by the answer, and I don't want to read it again.