The biggest problem that I see is identifying the equipment and runes. There would have to be an id of some kind assigned to each piece of equipment and rune so that they can be assigned to each hero. With equipment it can be automatically assigned when the equipment is bought from the armorer, but with runes you can not just assign an id to every rune that is created. There would have to be a way to identify what runes you consider part of your inventory and not the ones that you are going to use to upgrade other runes.

Then you have the problem of formations becoming obsolete when you take a rune that is part of a stored formation and use it to upgrade another rune. For example you have a level 7 purple one that you use to bring a gold one to level 6.