The word "flawed" is used in a deceptive way. Commonly, the alleged flaw is not really a flaw at all, such as Kirk's obsession with the ship---that's his motivation. Sisko's occasional ruthlessness is not a flaw but a fulfillment of tawdry fantasies about the need for a strong man to do the dirty work. Such characters are easier to identify with as vicarious fulfilments of assorted fantasies because the viewer actually approves of the alleged flaw.
The best example I think is Worf. Worf's aggressiveness (or that of Klingons in general) became an expression of a desire to be
aggressive/militaritstic/sexy, suitably displaced onto a fictional character with an elaborate rationalization within the fictional universe. But Worf in the earliest years on TNG was partly a projection of one of our real flaws, militarism. As such, his foolish ideas were treated comically, albeit affectionately. And of course his mere presence in the future showed the Klingons (we) would someday rise above our folly. It is very common for people to dislike this Worf because it demands a humane acceptance of human imperfection (despite our commitment to the good.) The modern Klingon concept developed in later years is much more popular precisely because it does not require people to identify with flawed characters.
The complaint about perfect characters is a complaint about the lack of virtues the complainer identifies with. In practice, the most offensive characters are not winners. Harry Kim on Voyager is quite a pleasant person, competent in many areas. And in a crisis he displayed heroic virtues. But in ordinary life he was well, ordinary. Tom Paris was allegedly the bad boy, and sure enough, Tom Paris was the sexy one. (Or would have been if McNiell were a better actor.) Chakotay didn't kick the bith to the deck, so Chakotary was weak, therefore unpopular. The classic objection, that Picard was too preachy was a complaint that he wasn't mean enough to get into fights, because poeple like men who win fights. The objection to Archer is that he didn't win more fights, because people like men who win fights.
The increasing trend to flawed characters in SF is pandering to baser elements in the audience. It is also dumbing down, because the kickass hero winning is just another childish fantasy. This kind of hero also suffers from the supposed defect of the too perfect hero who lectures the benighted. The "flawed" hero is invariably sexier than the one he/she beats!