Okay, next pass is ready.
5.5/2.1mm power jack. Mini USB-B for Serial. Crystal/capacitors for clock generation. Full Shield compatibility (standard complement of Arduino pins). RS232 for Serial1 with 4-pin header (Rx1,Tx1, Gnd, 4th is open). Rx/Tx jumpers to disconnect from driver if need Digital I/O or INT0, INT1. INT2 available at D6. Jumpers to select between A4/A5 and SCL/SDA at analog shield header. Two pins added to analog shield header for A6, A7. New 8 pin header for PC0-7 (includes SDA/SCL, even if jumpered to A4/A5). (hmm, looks like I lost an I/O pin for PD7 along the way) SD MMC push-push with dedicated SPI SS line not available else where on the card. Ladyada style design with Write Protect, Card Detect signals. Seperate 3.3V regulator for SD card. FTDI FT232RL USB chip with 3.3V to shield. ICSP header, allows BIT Bang programmig with FT232RL X3 header. 10 pin JTAG header. Power LED, "L" (D13) LED, Serial Rx/Tx LEDs (not on Serial1). No onboard reset - connect externally if needed (at shield pins, at ICSP, or at JTAG) (tho it appears there is plenty of room to add one, guess one pass to put pads in for it).
My only concern is the USB connector - any one know which library part to use that will let what appear to be the shield pads get connected to ground in Eagle? Here's close up of what I have now.