First, in terms of telling interesting stories, it is limiting. In HQ it is all well and good to be a master swordsman, but you are bound to face all sorts of situations that can't be well solved with a sword. Of course as a narrator you want to give players challenges that interest them, and part of the way they tell you what interests them is in how they design their character. But even the Three Musketeers solve a fair number of their challenges through knowing people, being charming, bravado, and so forth, and not always with their skill at blades. In HQ it is not just "I go ask Fair Isabelle for her help" and have the narrator decide if she helps, it is more apt to be a relationship roll to see if, and how much, she'll help.
Second, it can actually be counterproductive from a munchkin point of view too. Note that the difficulty level of challenges is relative to the characters, so being a master swordsman doesn't mean that you will win more of your sword battles, just that you'll face more challenging duels. This is a really key difference between HQ and many systems, rather than first defining the stats of the world then inserting the characters with their numbers, the system first defines the character stats, then builds the difficulty of the story challenges around them.
And if you follow the variable resistance system as written (at least as I understand it), the resistance scales more to your best abilities, so if you have very large differences between your best abilities and the rest, you actually have much less chance of success when you can't use those best abilities. So from a munchkin POV, to be able to use all of your abilities most effectively you actually don't want huge gaps between best and worst. (granted, we all like big numbers, and being good at something, so who isn't going to be better at something cool? But throwing all your eggs at that ability is probably counter productive). It is like being skipped ahead a grade or two in school because you are really good at math….what happens when it isn't math class?
Finally, as your flaws scale with your abilities, the better your best ability, the bigger your biggest weakness is. And with a very narrow base of abilities, your ability to work around that very bad flaw is much reduced.
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