The Linux installation got easier, but from a Desktop user's point of view features did not change much since '98 as far as I remember. Sure there is now (serious) support for all the new fancy Hardware like Webcam or SMP Processors. (I'm having doubts whether it's correct to say that Audio improved^^) But OpenGL was always there. Actually SDL was very popular during that time (SDL = OpenGL + X ~ Direct X) Interesting, I just read that it was actually Loki who developed it in '99 -- all their games were SDL based.
Otherwise you're right, setting up Linux Gaming computers with working OpenGL Hardware Acceleration was painful, especially for us poor people who could not afford the most expensive OpenGL Hardware. ;) On the other hand I think audio was easier to setup :P