I'm going to try to address the many issues swirling about this series without spoiling the plot:
1) Similarities to other shows: There has been a great deal of speculation that the show is a 'ripoff' of Battlestar Galactica, Firefly, or even Lost. While I certainly don't disagree that it bears a striking similarity to Battlestar Galactica, I don't count that as a strike against it.
Prior shows are always going to have an impact on future shows. Film-making (whether it be TV or Feature) is an art that builds upon itself, and stands on the shoulders of those who came before it. The fact is the Battlestar Galactica, Firefly, and Lost are all GOOD shows, regardless of your impression of it or whether or not it struck you the right way, they were the best of their genres at the time, and even bent their genres into something new.
That being said, to call this show a 'rip-off' or 'carbon copy' of any of those shows is grossly over simplifying things and intentionally misleading. Perhaps we should just create a new genre name, like 'Adult Sci-Fi', so we can get over all these intellectual property theft allegations.
2) Dissimilarities to other Stargate franchises: This review will probably take a lot of heat for this, but - past Stargate shows actually weren't very good. Don't get me wrong, I've watched every episode of SG1, and most of Atlantis (still working on that), and enjoy just about all of it, but even while enjoying it, I was fully recognizant of the fact that it wasn't actually good. It's campy. The acting is sub-par, even when there are good actors in the shows. The sets are generic and bland, reminiscent of the original series of Star Trek, the scripting is packed with fromage, and the plots, no matter how original, were all clearly predictable.
But to a niche crowd (myself included) they were thoroughly enjoyable through a mixture of silly humour, sci-fi gratification, and a unique self-aware self-deprecation. But even so, the cinematography was regularly lackluster, the effects unconvincing, and the ratings carried along by loyal fans.
SGU lacks most of these shortcomings. There is the occasional campy humour, though typically coming from the same character. In that way this one character, Eli, has come to be the only vestige of the old Stargate franchises. This is made believable, though, because this character is quite similar to the people (like myself) who enjoyed the camp of previous Stargate in real life.
3) The mood: Many would say it's much too dark, both in production design and in mood. I say that it's about time. In past Stargate series', no matter how far gone a situation was, no matter how much danger they were in, the show was never EVER tense. It never mattered. Nothing ever really mattered. The characters were always too happy and fun and funny and confident and amicable to be capable of expressing any kind of peril. As such, the plots were always completely hollow. Nothing mattered, because it would all be fine in the end.
The only episode in both original Stargate series' that managed to capture any kind of deep emotional commitment or tension was Heroes, which just happened to be filmed in the documentary style similar to that of SGU. I don't solely blame the cinematography for this effect, though, but instead, for just once, the characters were encouraged to be vulnerable and hurt, like real human beings.
When people are in a serious situation, they get serious (mostly), and their flaws become more apparent. This is evident in this series, as it should be in such situations.
4) The set/production design: As for the dark set design, it makes some sense, as the ship is very old, and trying to save power. In past Stargate, no matter how old something was, it always looked like it was cobbled together the day before. The ancient city of Atlantis looking like it was maintained by a team of maid-bots and carpenters right up until the team's arrival. I will admit that the purposeful gloom goes a bit too far at times, but as far as I'm concerned, that's better than skirting the edge of cardboard box grade production.
SGU is simply a great show. Yes, it shrugs off its past franchise for the sake of its artistic intent, but it does so with wonderful results. The acting is largely superb, and even the episodes that in other shows would be considered 'in betweeners' come off as being some of the best episodes on television (like the episode Human).
I definitely recommend this show to anyone, and I absolutely recommend that past Stargate fans try to leave their preconceptions at the door, and respect it as its own show.
UPDATE: You will no doubt notice a massive spree of negative reviews on top of the 'helpful' pile on IMDb. Please take these with a grain of salt, as they are largely spam generated by a select few alienated Stargate fans who are working very, very hard to get this show cancelled. Rest assured, I myself have yet to meet a single classic Stargate fan who doesn't LOVE SGU, and I sure do know a lot of them!