To start. I hope you don't give in to converting the game to a standard RTS where you defeat the level. I also LOVE the trash component, because it forces me to manage my colony well or every thing becomes a big slime fest (and no, that doesn't mean lots of burners).
But I did see one complaint and your response to it that I believe can be handled better, because you have all the pieces already.
The complaint was that moving from one map territory to another with more resources and more buffs than the first region means the game gets easier as it progresses not harder.
Here is what I propose to address that complaint
1. Rather than using the Main Menu targets to open buffs on the main screen, make them a requirement to open the culls gate.
2. The targets should increase with each region that is completed.
2. Rather than having the fight to be alive be for grins, make every day you stay alive after opening the gate an additional day for the couriers to work (if they or and the gate have not been destroyed)
3. Of course the monsters need to get geometrically more difficult rather than linearly after you open the gate.
4. Upon opening the cullis gate you get to choose from 1 of three permanent buffs, the monsters get the other 2 as permanent buffs.
5. Each region has the buffs and cullis gate targets predetermined and displayed thus adding a strategic choice for which regions you choose to start in/move to.
This seems to preserve the rise to RUINS... but also provide reasons for region selection and for striving to survive as long as possible.