My thing with the Incompetences, is that they are 5 point negative qualities, the minimum costs. These
shouldn't bite you in the ass every single game session, IMO. Like, a Mild addiction, it says once every few days/once a week or so, a craving should come up. Now, it's not a hard or fast rule...if the character is, say, at home for two weeks(hypothetically), with no 'pressure', it might not come up. Likewise, if said character goes undercover in a Jazz Ring and he's mildly addicted to jazz...then the craving could come up more often.
an Incompetence, IMO, should hinder the character once in awhile, for 5 BP. Now, a 30 BP negative quality? Yeah, that's a nasty one. Be prepared for it to really hit you hard. In fact, I might suggest against this because some qualities just hose a character soooo bad.
Personally, i like self-policing qualities. First Impression? Great, every time you meet someone the first time you get the bonus. It's nice and cut and dry. Allergy: Soy is good; my character that has it, the GM agreed that I pay an extra 10% a month on my lifestyle, I make sure myself i run a minimum of middle(if i got dropped to Low i'd probably add alot more), and basically make it a point of knocking extra off my nuyen if we go out to special dinners. It works well for all of us, and trust me, my wallet feels the flaw, especially since said character has a Suprathyroid. Yeah, +20% per month, baby. This adds up to 1k per month middle, and 12k per year. Basically, his allergy and ware cost him three lower priced runs. When you think about it in that term, its a pain in the ass. (should i increase to High? Double that.)

Allergies to Unobtanium are harder, since the GM has to be able to realistically stick them in sometimes. I mean, putting The Man with the Golden Gun into every blessed fight because a character has a mild Gold allergy is kind of lame; but an enemy that does a little research and remembers this can haunt them now and again. Sunlight is a great self-policing one, too. Go out during the day without protection, you're gonna hurt. Occationaly the GM can set it up where you are gonna feel uncomfortable.
Anyway, im also in the boat of rather allowing 50 points of really cool negative qualities that mix together, instead of 15 points of ones that don't. I'd be much more likely to allow Scorched, Simsense Vertigo, Sensitive Neutral Structure, Mild BTL addiction(all matching up), with other ones that might head into that mental screw category that add up to even 40 BP; but if someone tried to get Incompetence: Chipmunk Breeding and Mild Allergy to Elephant Liver past me for 10 points i'd of course tell em to pick something else.
I DO, however, give players the benefit of the doubt most of the time. I have a very, very, long and patient fuse when it comes to the 'twinkslap' (is that another form of pimpslap?

), and i very, very, rarely use it, unless it's said extreme circumstances.
All THAT being said, we stick to the +/-35 just because of simplicity purposes. It's a pretty big chunk BP to spend on qualities if you only purchase them, and thus should get something good, and it's alot of BP if you get it back in pure points. Works fine for us.
I understand it's not a disadvantage if you don't suffer from it, but there are reasonable ways to do this. I admit im not too into the ''If this quality does not affect you for exactly'' *gets out calculator and plugs in numbers for five minutes* ''At least 8.324444522 percent of the time in the game, i'm afraid i can't allow it. It's free points in that case, and i'm getting...7.99836 percent of the time. Please pick something else.''
I'm not saying anyone here does that, and it is greatly exaggerated of course, but I HAVE, sadly, seen GMs that ALMOST take it to this point where they are, for lack of a better term, 'quality control' freaks. If one of my players 5 point quality skips a week or even two where it comes up, the game is NOT going to implode on itself and fall apart.