If you've seen Scary Movie, it's the same sort of humor from that era. It isn't just shows from the 2000s, it's being a Millennial child in the 2000s that made it palatable.
Rewatching it now is really ugly. Kind of like that Marge Simpson story where her story is really gross, bizarre, and bigoted - a reference to the caricature of Apu - where you'd just find it severely distasteful.
12 Kingdoms, Rayearth, Escaflowne, and El Hazard were decent Isekai from what I remember. They're all from the 90s/00s though.
They still had trash Isekai in the 90s, like Those Who Hunt Elves.