1. Most instructions are run natively
I think this is the best method for any application
2. 100% emulation of the program with native OS calls
I do not undestand what advantage this method has over #1 or #3 :-?
3. 100% emulation with JIT
IMO this would be the best method for running games, creave a virtual amiga in the workbench, like winuae but integrated into the OS.