Which league was better: Serie A in the '90s or Premier League in the '00s?

It's really hard to say. I think the rise of Italy in the late 80's and early 90's was also indicative of exploiting a weakened continental field, as English teams were banned after Heysal in 85, at which point Italian teams did very well in both the European Cup and UEFA Cups during that time. The rise of English teams in the noughties has quite a lot to do with the change in the offside rule in 2003 (which actually favored possession based sides the most) as well as Italy reeling from the Calciopoli scandal in 2006.

I'd argue that Italian teams were better on paper up until the scandal. Those mid-noughties Juventus and Milan teams were absolutely loaded.

But the game after 2003 changed significantly. I'd argue English success in that time period was the fact that the PL had a mishmash of tactical styles, as it wasn't until Barcelona that teams figured out how to play the possession game negatively, and it wasn't until Bayern that teams figured out how to play a possession game with pace and power. I think English teams are much better poised for the next decade than Italian teams, but English teams still lack the tactical nous that teams from the continent seem to have in spades.

That said, I think the Serie A of the late 80's and the 90's was probably a better league.

...and their nucleus took the Dutch a long way, as well.