C'mon y'all. A GM needs to be flexible yet demanding. If a fighter takes "not subtle" as a flaw, then the GM needs to create a situation were the fighter will have to remove the armor and rely on stealth every now and then. Any flaw can be brought into play with a little imagination.
Sure, the player who is "heat intolerant" will hate the desert adventure, but did he honestly NOT see it coming when he created the PC and its background and choose that flaw?
If the flaw is allowed, it is the GM's responsibility to see it manifest in the game, not the players.
This is not to say a well balanced set of talents and flaws are not desired but the real problem seems to be more a problem of GM's not taking advantage of talents and flaws to challenge the player and create interesting events in the story.
Still, some setting or story archs may not allow certain flaws to have any real impact, in which case the GM needs to forbid them. An example in my game, all non spell users recieve "power burn" as an inherient flaw. Magic is dangerous and I try to convey that feeling to all players, because that is the sort of setting I like. It also results in non spell users being less than eager to seek out tons of daily items (note that an inteligent item that cast spells doesn't cause power burn, providing a good reason for faithful types to allow their soul to be bound to a magic artifact, or the less scrupulous from binding spirits against their will).
lynn