Straight up numbers comparison:
Augmentations
Skilljack @ 20,000¥ per rating
Skillwires @ 20,000¥ per rating
Activesoft @ 5,000¥ per rating
Knowsoft @ 2,000¥ per rating
Linguasoft @ 1,000¥ per rating
Priority Character Generation
Skill @ 1 priority point per rating (equivalent to 2,000 nuyen during character generation)
Karma Character Generation and in-game advancement
Active Skill @ (rating * 2) karma per rating
Knowledge Skill @ (rating * 1) karma per rating
Language Skill @ (rating * 1) karma per rating
The following assumes the full rating is purchased for Skilljacks, as the wireless bonus may or may not be desirable. It also assumes that no qualities like Jack Of All Trades, Master of None or its language and/or knowledge skill equivalents, have been selected.
Cost comparison for single Rating 1 skill
Active: 45,000¥ for augmentations vs 1 skill point or 2 karma
Knowledge: 42,000¥ for augmentations vs 1 skill point or 1 karma
Language: 41,000¥ for augmentations vs 1 skill point or 1 karma
Cost comparison for single Rating 2 skill
Active: 90,000¥ for augmentations vs 2 skill points or 6 karma
Knowledge: 84,000¥ for augmentations vs 2 skill points or 3 karma
Language: 82,000¥ for augmentations vs 2 skill points or 3 karma
Cost comparison for single Rating 3 skill
Active: 135,000¥ for augmentations vs 3 skill point or 12 karma
Knowledge: 126,000¥ for augmentations vs 3 skill point or 6 karma
Language: 123,000¥ for augmentations vs 3 skill point or 6 karma
Cost comparison for single Rating 4 skill
Active: 180,000¥ for augmentations vs 4 skill point or 20 karma
Knowledge: 168,000¥ for augmentations vs 4 skill point or 10 karma
Language: 164,000¥ for augmentations vs 4 skill point or 10 karma
Cost comparison for single Rating 5 skill
Active: 225,000¥ for augmentations vs 5 skill point or 30 karma
Knowledge: 210,000¥ for augmentations vs 5 skill point or 15 karma
Language: 205,000¥ for augmentations vs 5 skill point or 15 karma
Cost comparison for single Rating 6 skill
Active: 270,000¥ for augmentations vs 6 skill point or 42 karma
Knowledge: 252,000¥ for augmentations vs 6 skill point or 21 karma
Language: 246,000¥ for augmentations vs 6 skill point or 21 karma
More in-depth analysis:
It's fairly obvious that the initial investment cost is skewed way out of proportion for skillwires. That being said, depending on your reading of the Skilljack rules and whether or not one can make do with a rating 2 skilljack (which, if wirelessly enabled, arguably allows up to 4 skillsofts of rating 6 to run simultaneously), one can cut the initial investment by anywhere from 20,000¥ to 80,000¥.
Comparatively, then, the real difference between wired skills and real skills come down to cost of karma vs nuyen for the skill itself.
A Rating 6 Activesoft costs 30,000¥ which is equivalent to just 15 karma. This is 27 less Karma than the 42 Karma required to raise an active skill from Rating 0 to Rating 6 with in-game Karma, a 64.29% difference. The cost of purchasing a Rating 2 Skilljack and a Rating 6 Skillwire system (40,000¥ + 120,000¥ = 160,000¥, equivalent to 80 Karma) could be equalized by purchasing just 3 Rating 6 active skills (45 Karma vs 126 Karma, an 81 Karma difference that is the equivalent of 162,000¥).
A Rating 6 Knowsoft costs 12,000¥ which is equivalent to just 6 karma. This is 15 less Karma than the 21 Karma required to raise a knowledge skill from Rating 0 to Rating 6 with in-game Karma, a 71.43% difference. The cost of purchasing a Rating 2 Skilljack and a Rating 6 Skillwire system (40,000¥ + 120,000¥ = 160,000¥, equivalent to 80 Karma) could be equalized by purchasing 6 Rating 6 knowsofts (36 Karma vs 126 Karma, a 90 Karma difference that is the equivalent of 180,000¥).
A Rating 6 Linguasoft costs 6,000¥ which is equivalent to just 3 karma. This is 18 less Karma than the 21 Karma required to raise a knowledge skill from Rating 0 to Rating 6 with in-game Karma, an 85.71% difference. The cost of purchasing a Rating 2 Skilljack and a Rating 6 Skillwire system (40,000¥ + 120,000¥ = 160,000¥, equivalent to 80 Karma) could be equalized by purchasing just 5 Rating 6 linguasofts (15 Karma vs 105 Karma, a 90 Karma difference that is the equivalent of 180,000¥).
Conclusion:
A Rating 2 Skilljack (with wireless enabled) and a Rating 6 Skillwire system quickly becomes very cost effective compared to raising those skills with Karma. It is my opinion that using wires can be highly efficient for character generation performed with Karma (or Point Buy), whereas in priority buy it will almost never be advisable unless one picks Skills E and Resources A, and maybe not even then.
Furthermore, the fact that Skillsofts have legal availability ratings in the single digit range (2 to 8) and relatively low costs (anywhere from 1,000¥ to 30,000¥), a Rating 6 skillsoft can likely be obtained in as little as a few days, a week at most. The equivalent Rating 6 skill when learned normally will take more than 3 weeks of downtime (less if an instructor is used).
The biggest drawbacks with wires as I see it is that you cannot use Edge with wired skills, and the maximum rating of skillsofts is limited to 6.
House-rule territory:
If you could buy Rating 12 activesofts (for 60,000¥) they would in my opinion be much more attractive options compared to the 156 Karma cost (equivalent to 312,000¥) as well as months and months of time needed to learn said skill naturally. This would raise the initial investment cost significantly, but it would still take an equal amount of skills to equalize the Karma difference.