All4BigGuns, it doesn't stem from wanting them to be all-round badasses. It stems from comparing a number of builds and finding out that the Augmented character did what the Adept specialised in better, and had added flexibility to boot. And then comparing the Augmented Adept and finding he'd do it even better, it slightly less flexibly. It might appear from reading the books that putting implants in an Adept hampers them. I can assure you that if you do the maths and compare like builds you will find it does no such thing. On the contrary, it makes for the most powerful builds, as you get to stack the bonuses of both. You probably won't be very versatile, but you will be rocking every bonus possible. The 50 dice (I think it was only 49 actually) Adept is an example of this, as they will be using bioware.
If, as Umaro says, adepts were specialists and Street Sams were generalists, everyone would be happy. But they're not.
I'm still tinkering with numbers for an augmented build to compare with JustADude's quick ninja and I think, in fairness, that will come ahead of it sort of and that's fair and how it should be... although what he's done with gaesa is mildly abusive (which given that its an optional rule may not fly at a lot of tables)... even then, the Augment will hit more often (in unarmed barely and at throwing by lots) and be more stealthy (quite considerably), be a better athlete, a bit sturdier... its the 'doing insane amounts of damage with bare hands/knives' that you can't really replicate with an augment. So, he'd do better in the specialisation of 'hurt people', worse in the generalities - and that works for me. But this is using two sets of optional rules, one in a manner most GMs would balk at, and using one of the few things Adepts do have genuine options on (i.e. unarmed combat). Plus this is without cyberware, for that truly stealthy feeling (cyberware would probably level things up on damage).
So... we have one case where it works (just about), but I've seen plenty where it doesn't.
Oh. JustADude's version will have an extra initative pass. Which is a fair advantage. I have to say, sticking gaesa and a Way onto Increased Reflexes makes it a serious plus for the Adept vs the Augment.
Oh, and Tsuzua - You're missing out that its a Dryad using glamour at least. I forget the rest. Might go look it up... seem to recall Home Turf is used as well.
edit: The Adept can add on dice from a mentor spirit and therefore this is another field where, as is right, the specialised adept will beat out the augment.
edit edit: Found it, halfway down this page...
http://forums.shadowrun4.com/index.php?topic=4610.30 - I can't find the minor biosculpting bit in the rulebooks, but if its right, we're back to augment beating adept. For a lot less. If it isn't, you get one more dice for the Adept, and I'm fairly sure it will cost more.