Marionette Possession lists it's save as 'Will', but it can only target willing creatures. Does the fact that it technically allows a Will save ever matter?
Yes, although you will never roll it at the time the spell comes into effect the fact it allows a Will save sometimes matters for interactions with other rules.
One situation in which the Will save matters is if the initially willing subject later decides it doesn't want to be possessed after all and is then subjected to Protection From Evil or another similar alignment appropriate spell. If the saving throw were 'none' then the Protection spell would have no chance of suppressing the possession. Since the save is 'Will', the victim is allowed a Will save to suppress the effect.
Another situation is when you have the Heroic Will Human racial feat. If no save were allowed, you couldn't spend a non-action bust out of mind control like an awesome person. But since the spell technically allows a Will save, you can.