Weirdly, I'm in a similar situation and I'm trying to figure out where to go. SKills A, Attributes B, that was easy. From there?
Magic C, Resources D, Race E - Your typical physical adept that was pressed into a special ops-type situation.
Race C, Resources D, Magic E - An Elf (It's always an Elf) with the Black Widow/Nakita/River Tan/Exe Ass Iris vibe.
Resources C, Race D, Magic E for a "cyberninja" type.
For basic CovOps, you only need about 10K in core gear (Chameloen suit with thermal dampening, climbing gear, lockpicks, etc), with another 10K in fancy toys (Cellular glove? Seriously?) that are more Mirrorshades than Mohawk.
Here's where I'm at, so at least we can commiserate in unity.
Attributes (B)
B 3, A 4, R 3, S 4, W 3, L 4, I 3, C 4, Ess ?, Edg ?, Mag ?
Active SKills (A)
Acting Group 4, Electronics Group 2, Influence Group 4
Automatics 4, Blades 2, Escape Artist 4, Exotic Ranged (Grapple Gun) 1, Gymnastics 4, Lockpicking 4, Palming 4, Pistols 4, Sneaking 6, Throwing Weapons 2, Unarmed Combat 4, Pilot Ground Craft 1, Running 2, Swimming 2, Diving 1, Disguise 3, Perception 3, Electronic Warfare 1, First Aid 1, Industrial Mechanic 1
(Has spent 10 Karma on Active Skills)
Qualities (+/- 0)
Catlike, Double Jointed, Natural Athelete
Code of Honor (Assassin's Code), SINner (National)
Gear (10,000 spent thusfar)
Chameloen Suit with Thermal Dampening (4), Goggles (1) with Lowlight vision, Climbing Gear, Flashlight, Flashlight (lowlight), Gecko Tape(tm) gloves, Rapelling gloves, Grapple gun with 200 m of microwire, Catalyst stick, two 100m Stealth ropes, two 100m Stanard rope, Lockpick set, Twenty plastic restraints, Binoculars (Optical), Periscope, Micro-microcamera, Sequencer (4), Keycard Copier (5)
POSSIBLE gear (10,000)
Maglock Passkey (4), Cellular glove molder (4)
Still hasn't picked up a Hardware kit or a Disguise kit, weapons, a vehcile, lifestyle, etc, but still has quite a bit of cash (40 or 30K for Resources D, +90K more if Resources C) if I decide to go cybernetic. The actual B&E skills of Hardware could use a bit of help, but the social side seemed more fitting (Being able to talk your way past problems with Con, Disguise, and Negotiation), with some old school lockpicking and new-school "Tech, open this for me" style. Seducing someone, then palming their keycard to make a copy to get you in, rather than brute-force hacking, seemed a better angle. Your covert ops agent may vary, of course.
(Sadly, I did lose Exotic Weapon: Parashield Dartpistol (4) which I'd love to have back, but it didn't quite fit.)
Regardless, what you have is a generalist that focuses on stealth but can also work with a team (Decker for hitting locks, Cyberguy for hard combat, etc) ... heck, with a bit of skill tweaking, you could use the Covert OPerative as a basis for a whole professional Shadowrunning team, with other members having a different specialization but also a general coverage of stealth and the like.
So, you know, I'm sort of in teh same situation as you on this one.