Well, all the software available for AmigaOS today, from 1.x to 4.x assumes bigendian, change that and there will be major breakage. Which is fine by me, the opportunity can be used to fix all the other issues as well, memory protection and all that. And instead of integrated emulation to run old apps you would need a much more boxed solution.
An alternative is to go ARM which can be run in both bigendian and little-endian modes.