Billie doesn't use autotune. And the stuff he does on stage with audience members, that might bore some people who just want to hear him sing, are actually voice breaks. No human can sing for 3 hours straight, not even Billie Joe.
That being said,
I also dislike the overall sound quality of the Trilogy, and the amount of "filler " songs with less than ideal lyric writing. But as was earlier pointed out, I made myself a great playlist of all my favorites, so no problem. There really are some gems hidden on that set. They just sound like crap.