There is an old post titled "Antisocial characters" that goes on for sixteen pages with a lot of the debate centering on this exact subject. Several different opinions are put forth on how negative qualities or flaws should be handled, but I think the quote that reflects my position best is:
[quoteTaking a flaw isn't just saying "oh this is neat". It's saying "I like this and want you (implying the GM here) to make sure it's taken into account." Do you right up a complete background for a character and think, well it shouldn't come into play at all just because I wrote it? Do you raise skills and think, well I shouldn't use those new levels just because I raised them? Do you take edges and think, well this shouldn't come into play just because I bought it? Taking flaws should be answered just like the rest. They are on your character and should come into play.[/quote]
I end my games on cliffhangers most of the time. The first thing I do when I get home usually is to look over my copies of the character sheets and think of ways to bring characters skills, qualities (positive and negative), and contacts into play the next session. It's not metagaming, it's storycrafting based on what the players told me they wanted brought up in their character's stories. If the players don't want a quality to ever come up in relation to their character, they shouldn't take the quality. It's that simple. Kind of like how if the player doesn't want to play shadowrun, they shouldn't be playing shadowrun.
As far as how often and how forcibly negative qualities should be brought up, that is a question of play style. The same guy posted a play style guide that I found useful as well:
One thing you really have to nail down when you first start GMing a new system is what style of play you want, and what style of play your players want. Here's my general list of GM styles that I've played under/run:
God Mode: PCs rarely get scratched, they are practically gods.
Feather Duster: (Oh that tickles): PCs will occasionally take damage, but never more than a quarter of their health or they are considered seriously injured.
Action Movie: PCs will get shot up and hurt on a regular basis, but they don't die. When they hit 1/4 of their wound track left, they're horribly hurt.
Die Hard: PCs rarely die without a good dramatic reason, but they're used to walking away with one box of health and two rounds left in the gun.
Who's intestines am I tripping in: PCs die so often they're required to have multiple back up characters in case they "burn" through several in a session.
If your GM runs games in a play style that you don't enjoy, then you are never going to enjoy it. It doesn't mean he's playing the game wrong, it just means that you're playing the wrong game. I would fall in the
Die Hard camp. While I wouldn't enjoy a WIaITI game, I think I would enjoy Feather Duster and God Mode games even less.