The problem wasn't that the people had flaws, but that the flaws were either so massive that shouldn't have been in the positions they were in to begin with and/or the flaws were the defining characteristics of those characters. There's a certain level of competence to be expected from characters, and unfortunately for SGU, most of the leads aside from Rush rarely had it (except for plot relevant situations). We can buy people with flaws and who don't get a long as they're actually good/decent at what they're supposed to do, but when they utterly fail at that, we're gonna call bullshit on that.
1)I'm sorry but Rush's competence was too often overshadowed by the fact that he was the greatest bastard amongst the entire crew. Here was a guy who was willing to sacrifice people for his own ends (what he and I guess those that dote on him would describe as "The Greater good."). He was the most uncooperative, the most stubborn, the most likely to not be a team player. If you are going to be critical of the characters for not living up to your TV sci fi standards then how does he get a pass? Maybe you are one of those genuis idolizers, those Stargate fans who are drawn to the braniac individuals who in timely fashion figure out the impossible solutions in the last five minutes of each ep (no scifi series appears to have done as much to elevate the science geeks as Staragte). Hell, if so Rush should get your scorn. He doesn't even live up to those standards. Not that I'm saying he isn't a fantastic character because he is. At least a fascinating one.
2)Please, please provide me examples of the massive flaws that got in the way of these characters being credible officers. Because something tells me you may want to read up on the history of some of the great military leaders and some of the bravest soldiers in the history of humankind. Doing so you will come across people whose personal failings and stubbornness were only exceeded by their egos. And they still manage to get the job done...eventually if not immediately. The crew of SGU weren't perfect but in no way were they keystone cops.
3)Sometimes I wonder if some people don't understand that the writers intentionally had these characters fail and struggle. That they were not going to make these characters into the perfect individuals of TNG or SG1, the ones who got along, never showed signs of grey, always made the right decisions and told a thousand jokes along the way. Maybe I'm in the minority. I mean I love TNG growing up but I don't want to go back to that type of... "simplicity" for lack of a better word. While the internet forums were decrying Lt. Scott's whore-like ways, I found it refreshing to inject that trait within him. To be honest I'm not even sure it is fair to describe him as whore. He had the audacity to have sex on screen while on duty during the SGU premiere and then ditched his occasional hookup partner for a woman he actually developed truer feelings for. Oh. My. God. The horror. But wait! He had a son out of wedlock with another woman he didn't love back when he was a teenager!! That proves he is a sex-starved scumbag, right? No. It just proved he was an imperfect man who made mistakes when he was barely more than a boy. Big deal. Plenty of our bravest and finest fit the same description and are more capable and professional than most of us posting on these forums. And Young? He betrayed his wife and got an officer serving under him pregnant. Is that reason to be dismissed from the military? Yes. Is it enough for one to wonder about his judgment? Yes. Is it a definitive statement on his capability to lead, to make pressure decisions, to provide moral authority when needed? Nope. Thankfully in our world one's life and accumulated experience doesn't have to be discarded simply because of a few boneheaded indiscretions and bad decisions. Why should it be different for a TV character like Young?