Well, I've only played the allies, so I can't comment on it's use for Japan. But, I think it's pretty good when used for the allies.
You put backwater bases on auto convoy (all of AK, all of Central Pac bases, most of South Pac bases (Luganville and Noumea, but nothing north of that), all the SE Australia bases (no farther north than Sydney) And all the India bases up to Madras.
The system will supply all these bases without problems. Of course, the allies have all the supply you could want, so it does give more than a normal, efficient player would give. It also doesn't have to pick up oil or resources.
As far as the task forces routing through the Marshals, just watch the TF throughout it's journey. It will eventually route itself south and around the marshals (for those convoys going to Noumea and SE Australia.)
The only bases that you have to manually supply are Port Moresby, Lunga, Perth, Andaman Is (if you still own it), and the NE part of India. And you have to manually do your own supply hubs for future ops. (Pearl, Noumea, others??)
I think it's a great system for the allies. It'd be even better if you could put PG's and PC's into it.