Yeah the 90s overall were a pretty dire decade. I did enjoy some of it though - a lot of the Quasar run was fun (not the later stuff much), some of the very early 90s Avengers (at the end of the 80s/early 90s such as parts of Acts of Vengeance, Operation Galactic Storm), What If was still producing some enjoyable issues if you like that sort of thing, the later Captain America run, and Thunderbolts. And a few others that I can't quite remember. But as it went on it was mostly crap ponytails, leather jackets, earrings, stubbles, bad writing, bad art, and gimmick covers.
The 2000s were certainly commercially successful. The writing, art and print quality improved. Quite a few talented writers and even the bad stories still mostly looked better than the 90s. There was still a hell of a lot of terrible stuff - Ultimates 3/Ultimatum, OMD/BND/OMIT, Osborn doing Gwen Stacey, most of Civil War (a letdown in the end), Secret Invasion, Bendis disassembling the Avengers, a lot of X-Men stuff, a lot of the FF (just boring IMO) the Sentry mess, and plenty of others. Lots of letdown "events" where the plot went nowhere.
But I enjoyed seeing a lot of revamped characters come back and done well - Nova and the cosmic characters and Annihilation, GoG, Agents of Atlas, Iron Fist, and Thunderbolts was still a fun read. Hell they even managed to make Darkhawk sort of interesting.
However for establishing the Marvel Universe, and the introduction of important and long lasting characters, the 60s and 70s are hard to beat.