Walt
I have a small idea about the energy storage being able to store large batteries.
What if, you can change what kind of battery it stores. (Like the missile storage changing the kind of missile.)
If you set it to larger batteries, it changes shape, and stores a smaller amount of batteries. (Since they are larger, and it would balance it.) However, it would support all battery kind input, since small batteries would fuse into larger ones.
The big reason why one would want this option, is all about what it would be powering. If the energy storage is near a lot of small parts which needs less power each, one would choose to have smaller batteries.
If it is near a shield, or other parts which needs way more energy, one would pick the large batteries option, so crew travel less.
If it seems unbalanced in your opinion, you could make crew travel slower with larger batteries. (Which was mentioned before I believe.)
Hope you like my concept.