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.