I think there are enough good beginner books, I would like to see a reference book that explains the utter details, while at the same moment not being the AVR datasheet (~500 pages)
Some chapters could include:
- The Arduino core sources explained
- How to manage and modify I2C communication.
- How to make better analogRead's
- SPI for the not faint of heart.
- interrupts, software , hardware, ports
- Arduino over ICSP,
- bootloaders ,
-
A book - Arduino Assembler - "try this at home" series - would be interesting.
Beginner books are so ... for beginners

Hope this helps ...