The things I like about SGU are decidedly features that distinguish it from SG-1: no ability to go to Earth to get reinforcements/weapons (stones don't count since the number of bodies is still limited); mixed civilian/military crew; no aliens-of-the-week. My primary gripes have been about the pacing and characterization. Chloe was pretty much a non-entity until the blue alien thing happened. Rush has doubletalked and schemed and lied and kept secrets since day one and there was rarely a good reason for it. The civilians trying to take over the ship lacked a believable motivation since it was never discussed exactly how the civilians would run things differently--so it just looked like a petty power struggle over nothing. The use of the stones was downright laughable sometimes, like the nonsense with Young's wife.
The biggest objective fault in the show from the beginning was Chloe.
The rest? I honestly think it strengthened the characters and the storyline. None of it was arbitrary. You like the show structurally, but the biggest problems I've seen fans have in most cases (not all) isn't the structure of the show, but that they're unwilling to go with the characterization and the character development. SGU seems conceived as a slow burner that leads to explosions, and IMHO, has done more right than wrong.
Rush's constant deception? It was made pretty clear he's got massive issues. People who are paranoid don't need /legitimate reasons to hide things. That's what makes them dysfunctional. We got regular, measured insight into why Rush is screwed up as the seasons proceeded. The degree to which he is broken has set up Rush's overcoming his problems as a major struggle. It means something.
The civilian mutiny? Powered in part by a complete paranoiac (Rush) who was intelligent enough to instill his paranoia in others? The reason why the civilians wanted to take over wasn't because they had a totally different plan from Young; it was because Rush and Wray distrusted Young to make critical judgement calls in unknown situations. And why did they think that? Well...
... because Young has problems, yes. The stuff with his wife had a few moments of unnecessary complication (Telford's mini accidental affair), but it was a valid part of his development that helped create real, solid reasons for Young to fall apart under the stress of Destiny's situation. Despite the fan hate for the stones, their use for the most part paid off with character development down the road - especially in Eli's case, as the business with his mother really went somewhere and contributed to his maturing by a leap. (And from all appearances, seeding Eli becoming one of the most capable people for dealing with running Destiny on its mission; not just a survivor along for the ride doing the occasional helpful trick.)
The biggest departure SGU makes from Stargate isn't even really dispensing with four people shooting up a park outside Vancouver. Stargate never, generally, went in for this kind of long form, complex, and interconnected character development centric format. The SGU team hasn't executed it as well as it could be ideally, but what they've managed to do is still fresh and exciting. Made more so for the fact that unlike say, Moore's NuBSG, SGU apparently isn't trading the sci-fi and the mythology for the character drama. It's balancing the two, and even fusing the character development to the growing mythology.
Some of the fan rejection amidst all this has been outright head-scratching. Take the common sentiment that the first few episodes of SGU were "so terrible" because "nothing happened". Eh? Nothing happened except an actual science fiction scenario of survival in space playing out, where things such as renewable supplies, air, and even just plain water are not taken for granted? Concerns of over chemistry being major plot points? People on SG teams doing actual basic science on alien worlds, without technobabble?
Is it really so hard to see why some people have come away from the fan bickering with the impression that what a lot of Stargate fans want is limited to something pretty cartoonish?