I suggest starting in the middle (Being There or Summerteeth) and then working your way through the other stuff. I started at Being There and it was still a difficult beginning. I then got A.M. but haven't really begun to enjoy it until just recently. Now I see the greatness in each album...I don't really have a set favorite (although Yankee Hotel Foxtrot is probably the masterpiece), I have favorites at different times. There's so much good stuff there, even on A.M., the album newer Wilco fans (YHF and post-YHF Wilco fans) don't seem to want to get into (I have a number of friends who love Wilco but won't even pick up A.M.). Tweedy's songwriting -- lyrics and melodies -- are so good: direct, honest, insightful, poetic, sometimes ironic but always worth hearing. It's on A.M.; it's on A ghost is born.
To help the process of "getting" or "getting into" Wilco, I would suggest seeing the film I Am Trying to Break Your Heart and making it to a Wilco show if they come around. I Am Trying... really helped me appreciate Yankee Hotel Foxtrot, and seeing Wilco live a couple of days ago has really given me a new appreciation of A ghost is born. Sometimes it really does help to hear the songs in a little different context than the album.
I wouldn't suggest The Wilco Book to anyone who wasn't already a fan with a pretty good knowledge and appreciation for Wilco's songs and artistic process. That said, I really enjoy it.