In theory, flaws are good design.
In practice, however, players will take flaws during char-gen in order to get the corollary benefits and then do everything they can to ignore the existence of those flaws in play, or play around them, or cajole the DM (or, on a bigger scale, the game designers*) into toning them down or even eliminating them.
* - case in point: in the 1e-2e era char-gen ASIs had both bonuses and penalties based on what non-Human species you were, with the sum of those net bonuses and penalties usually coming close to a net zero; but players didn't like penalties, and so they were slowly decreased by edition and finally removed in 5e.