Yeah I think these are all great points.
The two things that are slated for a rework which will address most of this, imo, are auto-evo and AI.
So yes being a single hex of Thakyloids in a sunlit patch is an awesome way to survive, unless there are predators. And that’s what auto-evo needs to do, it needs to be always applying pressure to the player. As soon as you get comfortable doing something it needs to make other species which exploit you, much like your ocean example. So if you’re a photosyntehsizer it makes predators to hunt you, if you are a predator it gives your prey defences so it’s harder. That’s where the challenge comes from long term, imo.
There’s a roadmap here for getting it implemented and it’s not an easy task.
The AI also needs a rework, and potentially totally redoing. It needs to keep compounds away from you and be hard to hunt. It also needs to be intelligently aggressive and attack the player when it’s the right time to do so. As you point out there is a lot of room for improvement here.
Getting the spawning of compounds right and the amount of storage the player has is also important and it’s not quite there yet, though has had some work recently.
The issue of feeding into later stages is a huge one too. The absolute worst thing is if it’s a bunch of minigames where each one is forgotten when the next one begins. There’s a lot of things we can do in this area I think.
Anyway yeah you make a lot of interesting points. Buckly is the lead game designer and it’ll be interesting to see what he thinks about this stuff.