I always felt Waugh was a good captain, but not a great one like Taylor or Imran. He led from the front as a batsman and was fairly aggressive as well. Having said that, I'm not sure he's as innovative as people make him out to be. One stroke of genius I do grant him was placing Gilchrist as opener for ODIs. Still, I would back Ponting or Taylor on tactics over Waugh.
In my opinion, captaincy is best judged when you captain against either better teams or in tough conditions. With a team like the one he had, he should have been expected to beat other teams when cricket standards around the world were dropping, but he still lost to both India and Sri Lanka. He was given a run for his money by Stephen Fleming in 2000/2001 and nearly lost a home series as well.