I don't think either era really beats the other but rather they're completely different. The 90's with a bit of overflow into 88/89 were the birth of extreme metal while the '00s saw most of the experimentation on such genres with a few exceptions (like Gorguts or w/e being in the 90's). My favorite bands from the 90s would be stuff like early Incantation, Katatonia, Emperor, Darkthrone, Morbid Angel, etc. while my favorite stuff from the '00s is mostly progressive/experimental stuff like Blut Aus Nord, Deathspell Omega, Enslaved, Negura Bunget, etc. that can't be compared.