I've found a very simple system works pretty well for mook skills:
1. Set their "best skills" at Professional Rating +2. If they're really awesome at one of their best skills, give them a Specialty in it.
2. Don't give them more "best skills" than their Professional Rating.
3. Set "good skills" at Professional Rating. Have as many of these as fits the story / mooks.
4. Set their "average skills" at Professional Rating -1 (minimum of 1, of course). Have as many of these as fits the story / mooks.
5. Set their "bad, but still have 'em skills" at Professional Rating -2. Have as many of these as fits the story / mooks.
6. Add specialties for flavor.
How this often ends up working is I'll pick their "best" and "good" skills, then, if another skill comes up during gameplay with the mooks and I think "hey, they'd have that!" I'll toss a few dice at it, using the guidelines for "average" and "bad" skills above.
End result: you have mooks with dice pools that are competitive for their professional rating without exploding all over the PCs.