The issue is extremely easy to see. When you have magically active characters willingly, even gladly, sacrificing essence/magic then you don't have things pointed correctly. When you can get 2-4 times as much benefit from taking 'ware as you can from the loss in magic it is out of whack. A slight edge to the 'ware I think most people are fine with.
However 1.0 of essence (with no grades, no biocompatibility, type 0 system etc) gets you what would amount to 3.75 (basically 4) points of magic (more if it would take you into augmented levels). It should be glaringly obvious something is either over costed or under costed. Now the new ways reduces that from the 'ware being 4 times better, to only being 3 times better.
However this is only at base gear levels. If you push delta and biocompatibility that 1 point of essence becomes an even larger level of benefit. I don't know about other people play their games, but I have yet to play in one that nuyen did not accumulate faster than karma. Now compound that with an augmented character using nuyen to buy gear for bonuses, and then spending karma to raise abilities. Compared to a pure magical character only being able to spend karma to raise their performance. So on top of the just pure numerical advantage 'ware gives, it also allows the same double benefit that a street sam style character gets to take advantage of.
Then lets look at very end of life for characters. Unlimited money with 1500 karma. How many more dice is the adept rolling than the sammie? What 1 or 2? They will have same base skill ratings, same attributes, same gear bonuses, and same 'ware bonuses. So that puts the adept up with what 2 points via improved ability. The only area at which the adept exceeds the street sam is in close combat. Weapon foci for armed combat, and critical strike (and the adon abilites to killing hands) provide the only benefits that the street sam cannot duplicate. Hitting spirits/paracritters is an extension of this since an adept won't hurt them anymore than the street sam with ranged attacks, so that is tied directly to their close combat abilities.
So if you are going to do combat you go close combat or why bother. Now the bright side is with way of the adept you can get some really good noncombat adepts. Infiltration, physical ability, artistic ability, building/repairing things all got a nice boost. Basically bringing them inline with faces (what with their way specific powers duplicating kinesics bonuses), or providing mental attribute boosts. Faces still come out slightly ahead what with getting way discounts on their dice pool adding power.
Also the disparity has existed as far back as 2nd. I remember it being something like 53 karma extra to build an adept that matched the sample character street sam.
Saying all that. I do love my adepts. I will fight you tooth and nail to play one in a game. It goes to just being a cool factor. Still would be nice to catch a little bit of a break with them. Like if your magic rating actually started capped out like it did in 2nd. That'd be 65 build points that would help elsewhere. Push combat improved ability to 0.25 as well, improved reflexes to cost the same as the rating (1/2/3), reduce improved attribute down to 0.5 (and make it work for any attribute, and give the ways a discount on them for yanking their special ability), reduce pain resistance to 0.25. I would also like to see rapid healing add to peoples healing tests to heal you, like the quick healer quality, and reduce astral perception to 0.5 (always seemed a bit much at a full point). Also voice control should add the same dice benefits as the vocal bioware upgrade (same power point cost as essence, do the same things) has bugged me since I first got the Augmentation book.