I think most main characters in Star Trek are flawed somehow:
TOS Kirk seems larger than life and too perfect, but by TMP, he is flawed for sure. Ambition to take command away from Decker almost destroys his friendship with Decker, as well as jeopardizes the V'Ger mission. In TWOK, he is very flawed (how he deals with age, no win scenarios, his son, not raising shields). in TUC, he begins as prejudiced against Klingons.
Spock, more or less larger than life to most of the crew, but his internal struggle of his human half vs Vulcan half is a flaw of sorts. His coming to terms with it in the movie era post death is sort of a resolution to that struggle. In the TNG era, his conflict with Sarek is a flaw.
McCoy's flaw is mainly being too passionate and emotional.
Scotty, Sulu, Chekhov, and Uhura didn't really seem to have flaws per se, but their function seemed to mainly be followers.
Picard: definitely flawed in terms of dealing with children. It reminds him he may have sacrificed too much for his career by not having a family of his own. His unrequited feelings (not love, necessarily) for Dr. Crusher, at least until the movie era seem a flaw.
Riker: Usually a good leader, but I always felt that some of his suggestions to Picard are shot down as not the best course of action to intentionally show he is the "first officer" and not "co captain" of the Enterprise.
Data: Almost larger than life, save for his lack of emotion, and his quest to be more human. Once he does have the emotion chip installed in Generations, I think he has a hard time adjusting to emotions. By First Contact, he is shown as being able to shut it off at will, and by Insurrection and Nemesis, Data is largely characterized as he was before the emotion chip. So does this mean he has failed in his attempt to integrate emotions? Maybe! In which case that is a flaw.
Worf: Flawed in the sense that his Klingon Honor seemed to clash with Starfleet ideals and obligations quite a bit. Also, he seemed a flawed parent, sloughing Alexander off to his adapted parents.
Geordi: seemed pretty well rounded, but his physical flaw is his blindness, and his personal flaw would be his love life.
Troi: Her main flaw probably would be that she is a Starfleet commander by rank, but has largely acted strictly as a ship's councilor so long, that she has neglected her leadership skills. TNG addresses this in later seasons.
Dr Crusher: I think her main flaw was that she was not detached enough. Being a doctor, she seemed to let her biases and emotional connections get in the way of her voicing her concerns to the captain a little too much.
Sisko: Definitely flawed in the beginning. He was a broken man after his wife died. Other than his obsession with Eddington, he had few flaws throughout the show. By the end of the series, after being revealed as half-prophet, he is almost larger than life.
Janeway: I felt she was overconfident and heavy handed in the beginning. Also, her application of the prime directive was inconsistent: at times she followed the letter of the prime directive too literally rather than the spirit of the PD in some cases, yet disregarded the PD in other cases.
Archer: His flaw is being too naive in the beginning. Also, I think his prejudice and resentment towards Vulcans clouded his judgement in the first 2 seasons.
T'Pol: Seemed a little too emotional for a Vulcan (aside from her Trellium addiction), but I chalk that up to the fact that had the show gone to fifth season, we might have seen her revealed as half Romulan, which would have explained much of that. Then again, being in her 60s, she was relatively young for a Vulcan, which also could explain her emotional reactions.
