A lot of those achievements were in spurts. India won that series at home against Australia, but drew in Zimbabwe (most teams gobbled them up even then) and were decimated by the Lankans, and then crushed by the Saffies, only to bounce back on excess home advantage against a weak English side that frustrated and scared them. Against Australia, their performance declined, as after 35 years, they lost a series at home to Australia. Then, they nearly let square a series against a weak Saffie team, then let square a series against Pakistan, then England. Their home advantage began to wane tremendously in the 2000s, while their advances away from home were practically nonexistent outside Pakistan- until the very controversial Greg Chappell took over, and after he left.
In comparison, Azhar's team was virtually unbeatable at home for a very long time, in Tests as well as ODIs- with the only real competition coming from Sri Lanka and Pakistan. They were pushovers away from India, dubious selections notwithstanding, but that was a time when most teams would struggle outside of home or similar conditions. The kind of home advantage that Azhar's team possessed just doesn't exist in the Ganguly/Dravid/Kumble/Dhoni teams of the 2000s.
Moreover, a whole lot of talented players were lost in the 2000s, particularly lately. While some 1990s selections were quite dubious, we'd often see the best team play most of the time, and good players worthy of a long run, brought back after an absence. Here, so many players have been scrapped virtually for good, even with the replacement not being good enough at all.
