One of the aspects of FFXI concerning Puppet Masters I would like SE to implement is a system of saving configurations of automaton attachments. This would allow you to set a series of configurations suited for specific situations and drastically cut down on the set up time.
There have been many times that I'm using a DD auto then due to some freak happening that FFXI is so well know for, I'd need to change to a Healing auto or vice versa.
I don't believe that this would be game breaking because you would still have to take into consideration deactivation, Deus X, and Activation timers, but would provide many benefits.