The idea that Deans inherited the Wallabies as a shambles is just wrong. Yes the Connolly pack was destroyed by England but those flaws were left overs from the Jones era and the two years Connolly had were a hard ask to find and train new front rowers. What Connolly didn't do effectively enough obviously, was correct the woeful scrum & maul technique.
At the end of Connolly's reign was a time of generational change in the Wallabies with the retirement of Gregan, Larkham, Vickerman etc and even their immediate back-ups retired such as Whitaker. It wasn't so much a mess as a time of great flux, but it can also be said that most of those who retired were well and truly at the end of their careers. Deans got to rebuild from an almost clean slate.
The major difference is that Link is taking charge of a pretty young and stable playing roster, both capped Wallabies and other players available for selection. I think the oldest Wallabies are now Moore and Mowen, and both these appear to be at their peak and the other old head in Palu has ready replacement in Higgers. Is that a factor of Deans being national coach or the expansion of Super Rugby since the time of Jones with the Force and Rebels and hence having an additional (at least) 50 Australian eligible players exposed to top level Rugby.