Wow, many replies....
Garth, yes agreed on pin-outs as to not reverse polarity some voltages if the connector is plugged in reverse. I'm using shrouded/keyed connectors, so at least with the boards I'm building it's not an issue, but again.... just some good engineering. I'm planning to wire the dual-port connector mirrored more or less, so if you reverse it, you only reverse the ports
BDD, I'm already using a polyfuse on all of my boards, so agreed, a good idea. I'm choosing the 2691 to keep the size down as the board is quite small for this SBC. It's looking pretty packed so far, but it's still early in design. I have a 6551 running now as a console with the rewrite of SyMon code. I'll build a second I/O board for the 2691 chip and additional HW to interface it to the 65xx. So I won't be losing the existing console, just adding another I/O device, hence not flying blind.
Nyef, I did look at those other Flash memories some time back. Obviously larger than the 32KB I need for my small project, but they are inexpensive compared to the Atmel chips. I already wrote code to write the Atmel chips in circuit some time back so that's a small plus as well, but as noted probably quite simple to modify for these as well.