I like the concept -- very "back to basics" idea, hole through parts and all.
I think you could actually split this into three stages, building it up:
Stage 1: No USB/Attiny, no power regulation. Basically just 328p and crystal. Program via ICSP, or USB->TTY board.
Bring your own regulated power supply at 3.3 or 5.0V.
Stage 2: Add power regulation, but still have to program by ICSP or USB->TTY board.
Stage 3: Add USB/Attiny, can now program by ICSP, USN->TTY board, or USB.
Good work! 3.3V is a nice option.