Well, give them both a try! However, in my opinion they're intended for different audiences; AmigaSYS is clearly aimed at providing a complete Amiga solution (reflecting the large filesize and high requirements), whereas AIAB is more of a barebones setup for users to build upon themselves (again, reflected in the download size and minimal KS/WB 3.0 requirements).
If you are a registered MUI user, don't forget to copy your MUI.key over too.
Cheers,
James