I concede The Decemberists. Basically a band that blended the Athens Elephant 6 sound with 80s college rock. Sure: the Decemberists were more influenced by REM than by Patti Smith or the Velvets or Television.
Wilco is a weird one. I have a suspicion that Wilco, or at least Jay Bennett-era Wilco, is more influenced by mainstream early-90s alt rock than anybody is comfortable admitting. Heavy Metal Band is basically 1979 off Mellon Collie, which: what Chicago band is going to admit that influence?
Collective Soul, Better Than Ezra, Live: these are bands that kind of prove my point. The lead guy from Live once wrote Stipe a letter asking for advice on how to become a rock star.