Well you guys convinced me to try a minor priority swap.
Again the dice pools at Metatype C and Skills D:
Active Skills: Animal Handling 6, Archery 8, Armorer 3, Automatics 8, Blades 8, Clubs 8, Computer 3, Con 8, Cybercombat 3, Demolitions 3,
Disguise 6, Diving 2,
Escape Artist 13, Etiquette (High Society) 9 (11), Exotic Ranged Weapon (Grapple Gun) 10, First Aid 3,
Forgery 6, Free-Fall 4, Gunnery 8, Gymnastics (Dance) 15 (17), Hacking 3, Hardware 5, Heavy Weapons 8,
Impersonation 11, Instruction 6, Intimidation 6, Leadership 6, Locksmith 12, Longarms 8, Navigation 4, Negotiation 6, Palming 10, Perception 7, Performance 6, Pilot Ground Craft 5, Pilot Watercraft 5, Pistols 10, Running 2, Sneaking (Urban) 17 (19), Survival 2, Swimming 2, Throwing Weapons 10, Tracking 4, Unarmed Combat 8
And with Metatype D and Skills C (with 25 Karma being spent to get EDG 3)
Active Skills: Animal Handling 6, Archery 8, Armorer 3, Automatics 8, Blades 8, Clubs 8, Computer 3,
Con 9, Cybercombat 3, Demolitions 3, Disguise 4, Diving 2, Escape Artist 11, Etiquette (High Society) 8 (10), Exotic Ranged Weapon (Grapple Gun) 10, First Aid 3, Forgery 3, Free-Fall 2, Gunnery 8, Gymnastics (Dance) 15 (17), Hacking 3, Hardware 5, Heavy Weapons 8, Impersonation 9, Instruction 6, Intimidation 6, Leadership 6,
Locksmith 15, Longarms 8, Navigation 4,
Negotiation 8, Palming 10,
Perception 9, Performance 9, Pilot Ground Craft 5, Pilot Watercraft 5, Pistols 10, Running 2, Sneaking (Urban) 17 (19), Survival 2, Swimming 2, Throwing Weapons 10, Tracking 4, Unarmed Combat 8
With attributes (other than EDG) and resources being the same across the two, it pretty much seems like it did indeed come out to be a toss up. Advantage in the re-priority is higher Locksmith and Perception which are both skills the archetype uses a lot. And as an added bonus gains in Performance (via skill group) which is fun since since it helps give an explanation for why the Audio Analyzer cyberware might be there prior to beginning a life in crime.
OTOH the original build has more dice pool advantages over the respec despite having fewer skill points, because it has more Karma available to spend on skills. Where the original has a 2 dice disadvantage in Locksmith, it has a 2 dice advantage in Escape Artist. And advantages in several other secondary skills that'd probably be used often. The only real disadvantage I'm seeing is in Perception, as that'll be one of the most used skills for an infiltrator. And a tossup except for a point higher in EDG isn't much of a tossup.
In order for the higher skill priority to actually give a solid advantage, I'm gonna have to run with even lower EDG than 3 so that I can spend a comparable amount of karma on skills. That or get more extreme and go with the suggestion of dropping resources. But I'm liking the cyber; it's giving abilities that won't be replicated by some rando with a sneak skill and a mage backing him up with some sustained spells.
Some abilities the cyber is giving that isn't represented in dice pools:
Passive ultrasound (hearing motion sensors is huge for an infiltrator)
Ability to pinpoint location of (sound emitting) objects even while being unable to see them
Dampening from Flash Bangs
Noise Reduction
All of the above can be had via external/worn gear, but the following can only be done thru the cyberware:
DNI
Ability to squeeze whole body through any opening big enough to fit the head through
Ability to hold breath for hour(s) (immunity to inhalation vector; easy to use underwater terrain for ingress/egress/hiding while waiting)
And last but certainly not least, ability to know
anything that's plausibly ever been published on a knowsoft

Need to get inside a facility and do a task? Getting in is the first part. Doing the task is the second, and whatever task it is, surely there's a knowsoft relevant to that task! Besides, if you're using an impostor strategy to infiltrate, it's easier to look like you belong if you know what people who belong are supposed to know!
I guess a way to look at it is since I'm set on having a lot of cyberware, I'm building a snooty chromegirl specializing in infiltration rather than an infiltrator specializing in being snooty

I am still thinking though about maybe running with 2 EDG, and seeing if the extra skills that'd then be available make it more difficult to stay with the original priority array even with 4 vs 2 EDG. It'd allow for bringing the rebuild's skills up to meet the original's in every case (except Impersonation by way if being part of the skill group) and still have 8 more karma left over. That's a big chunk for even more dinky skills or even some positive qualities.
EDIT: I was thinking the best way to maximize the impact of 8 karma would be to look at positive qualities. And Oh. My. God. Friends in high places with 7 CHA is wringing a LOT of value out of 8 karma. And it's SRM legal... I think my decision to run with Skills C and only 2 EDG is a lot easier to make when I can have some uber contacts... Maybe pick a connection rating 12 and call her the black sheep relative of a Horizon Executive Board member

Hey I've already assumed for the background that the company already bailed her out by squashing a potential criminal conviction...