1.
Actually, my big wish for bases would be to be able to scrap the existing system and use the dev's map-building tools and utilize the various door mission maps as bases rather than blank cubic plots. More like AE than the current system.
Want to create a Batcave homage? Cave maps.
Want a high tech lab? Crey or Praetorian lab maps.
Want an abandoned warehouse (ala BATMAN 1966 show) for your villainous lair? Warehouse maps.
Want to keep the current blank cubes? Keep that as an option, too, by putting those assets into the map-designer.
Eliminate specific functions for rooms (regulate it purely on a maximum-#-per-base-size for power plants, inventory storage shelves, etc.
Eliminate item-by-item purchase cost on decorative-only items (to be included in the purchase cost of the map size).
Convert any (or most any) dev tool map tool item into having the core item/auxiliary item function you want. Maybe you want your power source to be a Croatoan pumpkin vine.
Finally, be able to output a base's design to a file on your computer (similar to current costume file or AE files) so you can back up your design, save different designs options, or even share them with friends.
2.
The second wish has to do with how bases are tied to supergroups.
My wish would be for any character to be able to a active member of one supergroup, and a reserve (or auxiliary) member of a second group (like your own solo SG), similar in comics of how a hero can be a member of more than one group at at time at various levels of activity.
You'd earn full SG prestige for your active membership group and half prestige for your reserve membership group.
You could participate with multi-player SGs and the group could build its base with your prestige, but you could also maintain and build your own private lair.