I think a great spot for the main base is near the southern thermal vent, where the grassy plateau, safe shallows and kelp forest meet. It's close to the jellyshroom entrance and not far from many of the late game locations. In the run I just completed I had four bases. One near the pod (5m), one in the Jellyshroom cave (300m), one in the Deep Grand Reef (main base, 500m) and one next to the cove tree (900m).

If you've found it, and if you have the depth capability, I think the Deep Grand Reef is a great late-game location.

This was my main base from my first run, and is next to the southern safe shallows thermal vent. Not much to go on, but you can see how it's against deeper water, but still shallow enough for solar power (although I used thermal from the geyser).

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Animals flee this hell, the hardest stones cannot bear it for long. Only men endure