Exploration is nearly impossible with the power level of the aliens. You have to be late game just to (Moderately) safely get rid of alien outposts. My current mid-game strategy is to run them over with a tank, get out mid charge, and start shooting with my combat shotgun while the aliens run after ...

Yes

Additional Z-levels might be fun, though I'd like more realistic biomes if there are. Native copper on the surface, Tetrahedrite underground with (More) realistic refining methods.

Mega structures could be created by 2x2, 4x4, or 16x16 versions of the smaller structures. For example, 2x2 assemblers which require construction robots to complete to create a mega-assembly. These could have internal buffers, require the proposed 'Loader' block for input and output, and have massiv...

I vote "God yes" On the Loader. At this point, logistics bots are almost infinitely better than inserter/belt chains in the late game because they're fast and hold multiple items... and after I have 100k logistics bots there's no point in having anything else.