Flaws are not just an easy way to get a few extra Skill Points, they are also a way for players to flesh out their character and tie the character to the mechanics of the setting itself. I think for this reason it is important for GMs to take a flexible approach with them and to be open to customizing Flaws as needed. At the same time before one creates a new flaw or alters an existing one make sure you are not creating more work for yourself and review the Flaw section in case something already exists that does exactly what you want (I've seen this happen to people on more than one occasion).
Flaws are also important balancers in the game. Players are getting extra Skill Points when they take them so it is important that they come up in play and not sit on the back burner. This is why a Flaw like Enemy has a 50% chance of coming up each adventure. When a player takes a Flaw in one of my games I always explain that doing so means that Flaw will create difficulties for their character during the campaign. It is going to come up routinely.
This is also vital to the flavor role of flaws. Flaws are not simply things we bump into once in a while in our lives, if they were they wouldn't be a defining weakness. Flaws are hurdles we are aware of constantly.
I strongly encourage GMs to fit the Flaw system to character concepts and not hesitate to create new ones as needed. I will give a recent example in my own campaign. It is set in a region where Sertori are vilified and the subject of much superstition. One of my players wanted to create a character who didn't now how to control his magic, was perhaps not even aware that he was a Sertori. As he worked on the concept he came up with the idea that his character casts spells unintentionally when he grows anxious or experiences other strong emotions. He has no control over his magic. There is a particularly clever twist to this that he added but unfortunately I need to leave it unmentioned until it comes up in the course of the campaign.
Initially when he presented this concept to me I looked to the Cursed Flaw. That would be a pretty easy way to fit his condition into the game because Cursed is quite broad and gives the GM lots of room to define. However that wasn't really his concept, it wasn't a curse, it was more of a profound personality quirk where he subconsciously casts spells. We also have a flaw for insanity but again this was quite specific and our existing Mental Afflictions don't really cover it (and I didn't want to create a new Mental Affliction which I might then have to add to the Affliction Table). Instead I came up with the following Flaw:
Subconscious Caster (Sertori Only)
You cast spells unintentionally when in the presence of a specific trigger. This may be because you simply do not understand your powers as a Sertori or due to an experience that causes you to lose control under certain conditions.
The trigger must be specific and ideally relevant to the character's background. It should be broad enough to come up during play but not so broad that it comes up all the time. Triggers could include things like hearing music, taking 2 wounds in a round, seeing objects of immense value, etc.
There are two basic forms of this flaw Minor and Major. The Minor form is less severe but only gives 1 Skill Point, the Major Form is more Severe and gives back 3 Skill Points.
Minor Subconscious Caster: You lose control and cast a particular spell in the presence of the trigger but otherwise you know how to use your Sertori magic and can cast spells deliberately in normal circumstances.
Major Subconscious Caster: You lose control and cast a particular spell in the presence of a Trigger. You do not know how to cast this spell normally, and can only cast it when the trigger occurs. Major Subconscious Caster can be taken multiple times to the point that all your spells are cast subconsciously (but you only gain 2 Skill Points for each Spell beyond the first).