First of all, I think you're confusing a good coach and a great one. A great coach is, as you put it, "one who knows how to figure out the best system with the talent he has and adjust accordingly" - but there aren't many great coaches in today's league. Gregg Popovich, Rick Carlisle, and Tom Thibodeau definitely apply. Possibly Doc Rivers if you're being generous. However, there are a lot of "good" coaches who were system coaches, and I can point you to many good coaches throughout the history of the NBA who have succeeded in one stop but failed in multiple future endeavors.
At worst, D'Antoni should be considered a poor-man's version of Paul Westhead - an offensive innovator who succeeded greatly in one stop but ultimately flamed out due to the shortcomings of his own system at future jobs. The league adjusted, it happens. But D'Antoni's mark is all over the not just the professional game, but the college game now as well. Considering the entire NBA has been adopting a variety of major elements from D'Antoni's schemes and playbook for years, it's hard not to at least lend him the credence of merely a good coach.