"My character is ready. What? Oh, I need to get some flaws to pay off all the extra stuff I've already picked. But my character is perfect... Now, what flaws would have least effect on my character?"
Sounds familiar? All too familiar to me. Most of my players want to think of all those munchkiny statistics and features first, and then, if the system has a mechanism for negative features (flaws, hindrances, disadvantages, whatever they are called), they try to find something that doesn't hinder their character. I confess, I'm guilty of that too.
Importance of flaws
Every good roleplaying game should have some kind of flaws. This is something that many think makes D&D less serious roleplaying game, especially as D&D players are often quite competition -oriented. Good roleplayers can create their own flaws for their characters and play them, but if efficiency is needed, they are quickly forgotten. But flaws are what make characters really interesting. If you are not GM'ing railroad-like adventures that have little room for improvising, they are even more important.
My recipe for this is that when you are creating a character, or asking your players to do characters, be sure that character personalities are created first - paying focus on those negative features. And mental ones are always more interesting than physical ones. It's even better if you create the idea of the character (flaws) without opening the rulebook. Once you have the idea of the character, you can translate it into game flaws and traits.
So, before you start to look for what the character can really do, you already know what miserable, flawed (interesting!) bastard he is going to be and have no illusion of a pure (boring) paragon character.
If you have doubts about flaws, just think of Galactica -series - character flaws create half of the stories in the series!
Risks for the game - killings and breaking apart
In case the players are in risk of killing each other because of their flaws (if using for example Conflict -encouraging flaws for Savage Worlds ) - remind them that their characters are people with only one life; killing allies (or people in general) may have dire consequences, either by law enforcement, other allies, employer or whoever has power in the game. And it may lead to character death, imprisonment, maiming - and often newly created characters get xp penalties.
And if the group tends to break apart, you perhaps should have something prepared, if you are not good in improvisation. An employer may order them to work together, perhaps using geas or implanted bomb if nothing else helps; Leaving character may really leave and player get a premade temporary character to play. Maybe something happens, forcing characters in the same location (Captured!), the bully gets punished by the employer and is pushed to find them and tell he's sorry, or leaving character(s) learn something that is likely to change their mind ('What, my wife has been captured in that castle?!?')
Game master's tools for flaws
Reward players for playing their flaws well and using them to create story. Depending on case, XP might not always be the best reward, but fate points, bennies, whatever resource mechanic your game uses. You may award special re-roll -tokens, or allow characters to recharge an encounter power after doing something cool but completely unnecessary, or something very risky. Make those character flaws, whether coming from game mechanics or imaginary, benefits rather than hindrances.
There's one more benefit from character flaws - they ensure you more screen time. If you have no flaws, you're likely to be left aside from what's happening more often than others.