Some ideas i’m just brainspurting maybe you can as well!
the ability to modify other creatures in later stages of the game: if you unlock genetic modification in the future stages you will be able to modify creatures, initially you use this to modify cells perhaps to aid in production (like a cell that produces nutrients that would benefit your agriculture) or for war purposes (designing a bio weapon thats a disease) later on you can use this to slowly modify other creatures until late game where you can pretty much design the ideal food production animal or other similar things
Smooth stage transitions:
Cellular to multicellular - the plan was to basically have the early multicellular play like microbial stage but just with an extra cell benefitting you however how does it transition from the 2D to the 3D? honestly i can just imagine it allowing you to tilt the camera but you’re still on a 2D plane then slowly introducing 3D movement
Multicellular to aware - apparently the transition (or atleast the old version) would’ve been signalled when you evolved a nervous system and gain sentience so i assume it’d play normally until the point you get too big to modify individual tissue anymore then you can modify your body.
Aware to awakening - apparently awakening starts out as just aware stage but you can now fuck around with random shit to try and see if you unlock something from the invisible tech tree so not really much i can suggest (the PDF already says that before you unlock the RTS control mode you manually order your guys around whilst still in third / first person perspective so you kinda got that smooth transition already down)
can’t really suggest transitions for the other stages because with the exception for early space stage (which i’ve been told is just Kerbal space program maybe you can still develop your technology elsewhere) you mostly are still in the “RTS” mode and the new stages are just new technologies (which ensures the smoothest transition possible)
when you reach awakening option to do silly mode - you basically can underwater civilization it up (optional feature added after release)
TU races being aliens you encounter - just brainspurting as i said
Dynamic destruction in the civ stages - you build your space ships and vehicles from building blocks mostly so just model a seperate damaged building block model or texture and convert your destroyed space ship / vehicle into that when they are damaged same for buildings except maybe they can collapse (like they did in old games where they’d just tilt and sink into the ground and a pile of rubble grew at their base)
procedurally generated story for space stage - this is either me misinterpreting what it actually said or it is what it said but in the game Hytale one of the gameplay features is that you are going on a quest on an epic story but still doing the usual minecraft survival mechanics basically during late or maybe mid space stage a story will be generated (like a genocidal enslaving alien race is rapidly enroaching and its up to you to try and stop them ) this could add fun to what might otherwise be monotonous space exploration (because at some point you would’ve seen all the varieties of planets and species possible and you haven’t really had a war in some time )
brainspurt over if you have other ideas you wanna spurt come join me