You pretend as if Australia just played in 90s, whereas the majority period of their domination was in the 2000s when they accumulated all those successive wins. The quality of the teams suffered and you choose to ignore that.
The WI teams Australia faced in 2000, 2003, 2005 and 2008 were quite poor, almost unwatchable aside from Lara. The NZ team in the 2000s was poorer than the 80s version which never lost a series at home that decade. The Pakistan team in 1999 was strong, yes, but they faced a second rate team in 2002 and a shambolic one in 2004, far poorer than the 80s version. England in 2001/2002 were comparable to their 80s counterparts, probably worse, and they lost to the stronger English side in 2005. And they feasted on Zimbabwe and Bangladesh, two minnows WI did not face.
India and Sri Lanka were definitely better teams than their 80s versions, but coincidentally Australia lost a series to both of them as well. SA remained a quality side.
So I don't think it's fair to say Australia faced tougher competition, at least in the 2000s. The three teams that improved (Sri Lanka, India, England) were the ones Australia managed to lose a series to. WI, as mentioned before, remained unbeaten.