Personally I really like flaws, however they need to be character driven, rather then point driven. If it's logical for a character to have a flaw, given his upbringing/training/heritage, then he should have it, whether or not it is used actively in a campaign. While this might give a PC a comparative advantage over another PC's who's flaws are actively hindering him, it does make sense in the bigger picture. PC's don't just live in the vacuum of the adventures the GM runs, they grow up, and if they survive the adventure, they live after it... there should be times in a PC's life (whether or not the PC is actually player controlled at the time) that flaws hinder him.
A Dwarf might, having been in mountains and underground his whole life, have a severe aversion to the sea... Now even if the GM's adventure get's no where in near the sea, so long as the PC has a chance to go to the ocean (and be sacred of it) during his lifetime, it's worth points. If there are no seas, or dwarfs would have to take over rival nations to even get access to them, then it's not worth anything. Much like if a fighter has no realistic way of getting access to spells he shouldn't get spell flaws, but if he's in a high magic world, and he needs to only spend DP's, then it's okay for him to take a spell flaw or two. (Some level 1 and 2 mentalism spells can be really effective)
Flaws shouldn't be tailored to the GM's adventures, they should be tailored to the entire world.
However GM's SHOULD try to tailor their adventures to play up flaws occasionally. If a fighter's 'not-subtle' make it so the group needs to sneak past big enemies occasionally. If a fighter is missing an eye (no depth perception) create a combat situation where then enemy can ONLY be attacked at range... You don't want to beat PC's over their heads with their flaws, but remind them they're there, and give the PC's motivations (assuming you even allow it) to use XP to buy off flaws they're getting irritated with.
Short Film: The Gamers- "Aren't you forgetting something??" "What?" "Your character's paralyzing fear of water perhaps??" "Oh yeah; AGHHHHHHHHHHHHHHHH!!!!!!!!!!!!"
One way to offset a PC who's got a lot of flaws that aren't getting action in the current adventure is to give him new flaws through the story. Make the PC hunted, poke out an eye in combat (assuming it can't be easily healed), have the enemy curse him with a flaw that can only be cleared at the NPC's death, give him a rival NPC, or talk a PC into starting a rivaly with the PC (provided it doesn't muck up party teamwork)
---------------------------------------
The biggest problem is that players usually grab talents first, then get flaws to pay for the talents. This creates a situation where flaws are point driven, not character driven. In some cases (especially with inexperienced players, or ones that tend to be powergamers) it might be better to present them with a list of flaws with no point values, and let them pick through them, finding things appropriate to their character vision... then let them know how many points they have to spend on talents.
Yet another line (this one more random) from the wonderful film The Gamers: "That's 15 Piety points per level... that's like 90 Points!!! booyaeh!" "Yeah, that will totally make up for that orphanage we burned down.."
