The "Design choice/Feature" still applies for the crystals. And why would you want to remove their ability to hold EU in the first place?
If energy storage transfer abilities are moved to energy storage blocks instead of the items, you can then have the items stackable.
Otherwise, it's a moot point.
Personally, I think the question should be changed to 'Should Batboxes, MFE's, and MFSU's retain energy when wrenched' instead of what it is now- As the EU storage of all other machines are quite small. A Mass Fabricator saving it's percentage might be nice, though.