I'll repeat everyone's advice and say: fill out a feedback form at Apple.com to request these features. From what I understand, Apple actually does take that feedback seriously. If you feel really strongly, try organizing a feedback campaign to encourage many people to send feedback on the same issue.
In the meantime, I'll try to address your concerns:
1. Nope. But Apple isn't alone: Goodreader and Stanza don't do this either. I think iAnnotate PDF does, but of course only for PDF.
2. If you mean what I think you mean, this feature was just added in the most recent version of iBooks.
3. Nope. But Goodreader does this extremely well.
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