Sounds like we're in about the same boat. I figured there wasn't much sense trying to keep shield-compatible an official (Arduino, Sanguino) board since the vast majority of shields aren't designed with power management provisions (no need to, since the Arduino pulls ~17mA idle on its own) - so while I'm doing my own thing, I decided to make it perfboard-friendly (leave that funny header spacing behind) and split the headers into 3 sections with the common bus signals (e.g. SPI, I2C, power/gnd) replicated for each.
Some libraries may have to be tweaked anyway (SD lib won't initialize a card more than once; necessary when cutting its power during idle periods), but hopefully they are in the minority!