Interesting, so setting up an upgrade system for the buildings.
Your selection of buldings remains the same (think of it as the hand you've been dealt) until you choose one.
We might need to add some more interactions that can help with utilizing excess resources. Perhaps let's start planning out how to add more depth to expansion.
It is really up to you how far you want to take Expansion. There are numerous world-building games that can act as a template, but I doubt that you want to be laying infrastructure like Sim City or having massive wars while building the Pyramids like Civilisation. I think that sooner or later anything you do should relate directly to Outerworld and Sanctum rather than just being a completely separate game-within-a-game.
In my mind, the most obvious new structures would be buildings that generate Creds and Expi (the blue stuff, not actual XP) for use in Sanctum. Maybe a blacksmith to make equipment, possibly made-to-order rather than randomly generated. Maybe the tree idea I had could live in Expansion instead of Sanctum, though the idea of a massive tree in Sanctum sounds pretty cool.
I had that scout idea. Maybe you could have a trebuchet or catapult instead. Aim it for somewhere on the map and it uncovers a small part of the map where it hits with about 20% accuracy. Only for uncovering the map, it wouldn't do any damage to any resource or building, friend or foe.
Maybe this idea of merging eggs could be done via a building in Expansion. Maybe even in Sector 2, so it is a while off for anyone.
And something totally separate and REALLY long term would be to do with the Souls. I don't know if they have a maximum level, but there could be some day the possibility of a Prestige system for individual characters. Maybe a +x% increase to stats as well as power & % chance of their spells and attacks. And maybe an extra connection on Orbs (so a Pentagon) and the Equipment grid becoming 3x4 or 4x4. But all this would mean returning to level 1.
And I had one last idea. You know we were talking about a bonus for having four of the same species of character on your team. How about instead of a passive bonus, a % chance of a mega attack, like Voltron or Power Rangers, where all four combine to perform a special attack. You wouldn't need special effects, just all four piled on top of one another would do, I think. That alone will be troublesome enough with around 120 characters, without making each into a unique being. Even the word MEGA ATTACK appearing on the screen with a picture like when they merge in Voltron, except the large middle image would be the Soulmancer and the other four would be the team members.
Another idea for expansion. In the same way that there are one-time-use caves, you could have some one-time-use rest sites or rest sites that can be used once every x hours/days. This is assuming that you haven't planned to add a rest site elsewhere. You could also have randomly appearing bonuses, requiring players to check Expansion frequently. These could be rest sites or even just randomly appearing Creds, Expi, Equipment, Eggs, Orbs etc.
Maybe add the tree that I suggested for Sanctum as a building in Expansion. This could cause these random bonuses to appear.
I think it might be an idea if the caves can be accessed every x hours/days as there is virtually nothing to do in Expansion. Having them be destroyed after one fight seems like a bit of a waste of a feature.