My point is, that it CAN'T work. You mentioned several reasons yourself. A lot of stuff is just dropped in order to reduce book-keeping.
Making the guy who pushes extreme in one area need close to no Karma while the person dambeling in several "hobbys" needs a lot if he or she changes those hoppys.
Dueto some other simplifications (common knowledge is 0) things get also out of hand, because the dicepools do not really live up to the expectations. (Perception is one of those fine examples. Two dice to spot something? Come on!)
So you can have several years of education in one area for 0 Karma, while a little knowhow in an other area costs at least 2/4 points.

There is a reason most games say: Zero means you have zero idea about it. Because there will always be a instand in which you match different skills against each other. And if one skill starts at "having not seen something like that in my life" and the other with "Done it for several years" it can't really work.

My mistake, I thought they were talking about Free Spirits draining karma as NPCs.

I hereby invoke the rule of Common Sense. No skill does not necessarily mean the character has zero idea about it. Also, one thing you do not seem to understand is that for a lot of skills the GM only needs to call for a roll if he/she feels the circumstances warrant it. Some examples:

1) Running ... Every metahuman can walk, run or sprint - the BBB's movement rates tells us this. Running skill is used only to increase the distance covered above these movement rates, or if the GM decides the terrain/visibility is tricky and calls for a test.

2) Pilot Ground Vehicle ... Most people can drive (if you call plugging into GridGuide and sitting back "driving"), the PGV skill is more an Advanced Driving skill than anything else. You might not need to even make a test if you are driving doesn to the local mall, but you will if you get involved in vehicle chase/combat situations, pull a tricky manouvre or for whatever reason need to make a crash test.

3) Pilot Aircraft ... Yes, this is one of those "no skill means zero idea about it" skills. Doesn't mean that if push comes to shove a runner cannot try and wing it (literally!) defaulting on Reaction, but I wouldn't necessarily recommend it.

4) Knowledge: Cooking ... For me the zero skill can mean different things depending on the character's background: some characters might think a saucepan is the wrapping around their favourite brand of Stuffer Shack soy burger, while others might be used to heating nutrisoy over a propane heater. Characters who take the skill will be developing their knowledge of how to make said nutrisoy taste nicer - Skill 1 probably leads to a basic knowledge of herbs and spices; increasing the skill improves the gourmet quality of the food the character knows how to make. Similarly, a socialite character who has drunk wine from time to time might vaguely know the term Cabernet Sauvignon even if he/she does not have a Knowledge: Wines skill.

5) Perception ... This skill is used to notice things that might not be obvious to the casual observer. If the character is ambling along under no stress looking for Vine Street, the GM can rule that they find it, no Perception roll required. If they are bombing along in a stolen car (with GPS for whatever reason turned off) at 100kph with police on their back, a Perception check may be required. The other thing you need to remember about Perception is the 3 dice bonus for Observing in Detail where appropriate, a big help to watcher spirits and PCs defaulting on 2 dice.

@Midas
Fact still is, it does not really work out. The second you have to call for a test, they will fail as if they would be unable to walk or anything.
Invoking a rule of common sense in order to defend a mechanism which is just broken, does not help.
(Of course you may just not use perception tests at all, but thats hardly a working solution)

And of course your whole argument goes for a ride to the sewers as soon as the rules give example thresholds for neon signs, or something else. What they do....

The point is, IT CAN'T BE WORKING. That just as easy to see as a neon sign in the dark.
In order to give a person with 0 perception, leaving him with about 2 dice, a chance of seeing stuff, you would need give him a lot of bonus dice for normal perception test. (For example to spot a friend in the crowed.) Around +5 and +8.
The problem is, that those boni would still be around, if you roll against infiltration. (Additional to all the modifiers against the guy using infiltration)
Making infiltration nearly impossible. (Simply because a 0 in infiltration would mean (like a 0 in guns) that you have no idea, while a 0 in perception means, you have a normal perception. Does not work, can not work.

I personally have Incompetent (Cooking). I can make scrambled eggs and ramen, and I burn everything else. I've even burned water.

Funny you mention that - I had a friend who once failed to boil an egg. How, you might ask. I did, turns out he let the water boil away and came back to the kitchen to discover the egg burned and half melted to the saucepan base ...

You think the mechanic is broken, I do not.

Taking your example of a person looking for friend in a crowd (INT 3, defaulting to 2 dice, your example):
+3 Observe in Detail
+2 Prior knowledge that friend is there or will be there soon (they had arranged to meet)
- 2 for the crowd
That would give him 5 dice, statistically 1.67 successes, he spots friend
Let's say they had not arranged to meet, he still has 3 dice and a good chance to spot his friend in the crowd if he is actively looking at the crowd; if he is intent on his commlink instead, chances are he won't notice his friend pass by, but it's not like that doesn't happen IRL ...

Than lets take a look in the book:
We can add to that, that he needs 2 hits for "pedestrian" and now we may add to that "Object/sound not in immediate vicinity" for abother -2.


So why should he do that? Be activey looking?

Depending on how you do it (and we did not add visual modifiers) you end up having 0 to 5 dice for doing that, while needing 2 hits.
(Even with 5 dice, the chance to succeed is 54%)
The only way to get around it a bit, is extended tests. But those come with declining dicepools as soon as there is the possibility to fail. (Which is mostly the case! And there are no rules for extended perception tests)

And if you are just walking through the steets you will probably NEVER make out a friend you meet by chance. Taking 2 dice for 2 hits means 11%.

You can be go on and look at somebody searching something in his room. Look for a lense they lost on the floor and so on. (Here was also the discussion, that normal drones CAN'T see people)
This leaves you with TWO options. The first option is to give a lot of "situational" modifiers to the observer. The problem here will be, that those will also apply to "rivial tests". For example to spot an synthetic cyberarm. Making those test easy as hell, as soon as you get your perception skill...