I share your feelings on collections (that's one of the reasons I love calibre so much). One of the things that drives me a bit crazy about the Reader is the way it considers books on the SD card and books in the main memory as two different collections. Since a lot of my collections are split that way, it's annoying. But without collections, browsing by title or author (another peeve: the Reader doesn't respect author-sort) would be a screaming pain, especially since I've got over 2,000 books on the thing.
As to your metadata problem, insert my stock rant about DRM here.