At present, the game stops if the player reaches one of the Victory conditions.  Consider giving players the option to continue playing until they've achieved ALL of the Victory conditions.

Having played Cardalaxy a couple dozen times, now, I've noticed something about the current Wellness mechanic.

Once the player has reached the first Wellness milestone, the Wellness decay mechanic pressures the player into investing heavily into Wellness to stay ahead of the decay.  Unlocking Health Tracking Centers and/or Modular Farms becomes a major survival priority for the player, as a result.  However, once either of those are unlocked, it becomes much easier to overshoot the Wellness decay and jump straight to victory.

I therefore suggest two changes:

1) Currently, the rate of decay is a function of the highest Wellness the player has ever reached.  Change this to instead be a function of the player's current Wellness; as Wellness drops, Wellness decay should also drop.

2A) Double the Wellness amounts required for all milestones OR...

2B) ...add more Wellness milestones such that Victory is still the last milestone, but requires 100 Wellness.

Increase the delay between a boss being defeated and the next one showing up.  Or, perhaps, have an (early-game-unlockable) toggle for aggressive/normal/defensive that makes all ships show up immediately/after one turn/after two turns.

"Can't replace a building with the same building."

While this makes sense in the general case, Space Mines need to be refreshed and thus should be exempt from this rule.

Either that, or just rework Space Mines completely.  The mechanic from your older game, "Planet Crafter" will suffice: 1 Combat plus 1 Combat for each other Space Mine played on the same turn.

First Wellness milestone sometimes presents the following two options:

"Cooperative Endeavors": Gains 3 Science when completing a missions and gain 3 Exploration when completing a Technology.

"Surplus": Gain 3 random points each turn.

Completing missions and/or technologies doesn't happen every turn.  The player ALWAYS gets more points in the long run by choosing "Surplus".  I suggest increasing "Cooperative Endeavors" to at least 8.