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.
yep, it's a very good idea to offer also a basic design, it would give newcommers a better understanding of what is essential for an arduino board.
There are plans for an ICSP port (because it is simply a must have). but sadly i didn't had the time to add it, but it is planned for the first update.
my plan is to make a pinout for the attiny2313 too and connect both to the ICSP port, so you have the abillity to reprogram both MCU's.
The other thing that would complement your design nicely is a small pcb layout, perhaps one that could be made to fit the size limits of the inexpensive "10 boards for $10" pcb board makers (itead/seeed etc.) Just a thought, if things could be made to fit. That would be a pretty slick "DIY Arduino" project, then, I think.