Tom Waits may look a bit more raggedy in his old age, but he's still inventing new ground to cover all the time, with each album he releases. And how many albums has he had released since 1990..? Like.. 5 or 6 maybe? Plus a number of musicals and operas he's written. For post-1990 innovation then check this man's shit;
The Black Rider and
Bone Machine.
There's a number of other post-1990 acts I can rave about here, though whether you could class them as original/innovative or not is an entirely personal opinion;
Jon Spencer Blues Explosion, at least for a few albums, came up with some of the strangest music you could hear, full of- but not limited to- neo-blues-psychedelic riffage, unwarranted and unexpected screaming, nonsensical rambling, theremin solos.. good stuff.
Orange is a good place to start.
I'd argue some of the best hip hop came out of the 90s- basically being the 'new wave' to the 'punk' of NWA, Public Enemy, et al.
Hello Nasty by
Beastie Boys and
Enter The Wu Tang by
Wu Tang Clan are couple musts. Hell,
Beck's
Odelay is some of the dust brother's best work.
As far as that, there's been fantastic singer-songwriters to come forward since 1990.
Conor Oberst, Chan Marshall, M. Ward. Some completely off-the-wall time machines like
The Squirrel Nut Zippers, Dresden Dolls, She & Him..