If the boards all use the same header, then shield compatibilty is sort of built in, yes?
Uno/Leonardo have same header assignments, Mega has all the extra pins plus SPI in a different place. Add some pads so SPI can be jumper selected from Uno's D10-11-12-13, or have wires brought over from Mega's 50-51-52-53 (or whatever they are) for max flexibility. Same header pins can be used, Mega needs D20-21-22-23 (whatever those are) set to inputs so 50-51-52-53 are not interfered with.
I or my wife have 1 or more of Duemilenova, Uno, Mega, Esplora, ProMini, some of the Lilypad things, Wifi shield, maybe couple more things (have to look), plus a lot of custom 328P & 1284P designs.
Only prominis have actually made it into a project, 10 or 12 or so before going full custom as seen here:
http://www.crossroadsfencing.com/BobuinoRev17/