The point isn't to make a "quirky" character. The point is to take ownership during the game. It sucks to make a character that seems like it should be apt for a setting and find that, solely because of the ruleset you are using, your character is inefficient, substandard, irrelevent, or bland when compared with other player character. It sucks because you know that if you were using a different ruleset, the character would be very apt for the campaign/run/situation.

The face is a good example. Shadowrun is a game where the face really shines because there are rules and subsystems to help support it. But in almost everyother RPG, the player playing the face either has to be doing something "quirky", has some kind of tacit agreement with his GM, or will be otherwise substandard at least half the time.

One of the reasons the face works so well in Shadowrun, also, is because he can overlap other secondary functions. He doesn't have to be useless in combat, or hacking, or spell use. This is a great aspect of Shadowrun. So long as he doesn't do all of those things too well.

A certain balance needs to be achieved. Sometimes I think Shadowrun's got it. Sometimes I really don't. I think Shadowrun has it more than other games though, and that's why it really stands out when something's off.

I blame the build point system. (No reason, I just miss priority charts...)

Contrast with:

Your uncybered mundane covert ops specialist is not weaker solely because of the ruleset and in contrast with the setting. An uncybered mundane SHOULD be weaker, that is consistent with the setting. You're blaming the rules for being consistent with the setting. In a different game with a different ruleset AND a different setting, an uncybered mundane covert ops specialist may be comparable in power level to anyone else. But if SR was using the same setting and a different ruleset that allowed for an uncybered mundane covert ops specialist to be comparable in power to their augmented counterparts, that's not a win, that's a failing of the ruleset to support the SR setting.

That said, while an uncybered mundane covert ops specialist may not be able to cling to walls quite like their augmented brethren, and while their dice pools will generally be a bit smaller, that does not make them an unplayable concept. You'll have plenty of extra BP to have good, solid skills in MANY areas, with an extremely high Edge to boot! You'll be totally inconspicuous under any cyberware scan OR aura check, no matter how high the person's initiate grade. And you can have a lot of fun playing his struggle to keep up with cyber-Joneses. You can easily make this character work, he'll feel a bit underpowered, but he'll make up for it in utility and and versatility.
I have a character a lot like this in a campaign that I'm running. She doesn't rule combat, in fact she generally avoids it or just takes cover and takes a few shots to keep the enemy dodging, but no matter what the team's doing she can at least help out, since she has skills in everything, and while she can't outperform anyone in their specialty, she's got a high edge and knows when to use it so her part of the plan, no matter what it is, always goes down without a hitch.
SR4 is the first edition of SR where the uncybered mundane is playable. They'll never compare in power to the cybered or the awakened, and that is good and right and consistent with the setting. They will never be the choice of the powergamer. But they are very playable, if you play to their strengths, and make a fun character who will always have something to do.

Both of them, and neither. The whole key here is that both of them, and the rest of the group, and the GM need to come to a mutually agreeable solution to this and any other "problem" in the game.

And I don't really think you can assume that all things are equal, because if they were there would be no imbalance. Both players would either have "normie" characters or "uber" characters. I have yet to see a situation in which there are two equally adept power gamers, but one creates a character that can't compete or contribute and is then upset that the other guy's character is stealing the show.

Thankee-sai. The lesson is learned.

...bingo. As a player I often do this. It doesn't bother me that such characters may be "less effective" than a dedicated "monster". What doesn't sit well with me is (as I mentioned) when another player purposely goes out to make the character useless because "they" do not like the concept or want the spotlight all to themselves.

The original KK had only 2d6 of initiative. a shortcoming, sure, but she was also heavily focused in melee which gave her a huge advantage because of the old counterattack rule. Coupled with her athletics and stealth, she was able to get herself into a melee situation most of the time. When gunplay broke out she would take her shots then dive for cover or try to get herself into a more advantageous position. Playing her required a fair amount of resourcefulness which is what made her fun. This also contributed to developing her personality. When I ran a total min-max combat monster for one campaign I found it rather boring and the character was very two dimensional because there really was not much of a challenge.

Last I heard it was 4.3....

...the original KK was SR1 - SR3. This inception remained pretty much intact throughout her career with minor changes when things like powers and skills changed with each new release. The biggest "revision" was rebuilding her under the BP system in SR Companion. With a few minor differences, she remained pretty much the same character.

The "4.x" designation came into use while our group was learning the SR4 system and I generated a totally new version of the character. There was no way I was even going to attempt converting the original character considering she was about 300 karma prior to SR4's release and we all thought it best to use starting level characters. Each ".x" was a revision as we developed a better understanding of the rules and were allowed to "re-tune" our characters.