I'd actually welcome different styles of playthrough, which I believe was a game goal at some point. Where you research one of a mutually exclusive set of topics very early in the game that radically change how your crew is going to interact with the world. Being outright heroes could be fun, or actual villains. Aligning with different groups with different ultimate goals.
Something I'd also like to see is us actually being required to set up the protection racket we have going on, though for that, I wonder if it's possible to have base buildings either closed off and without any maintenance or lowered maintenance but with lowered utility. Both unlocked through research or manufacturing. The lab especially, you're not going to turn on the mainframe until you finish the research related to it, so the maintenance for the lab could be far lower before your brainers figure out the plug.
The prison, barracks and store room could have lowered capacity until you put your runts towards cleaning them up and repairing what is broken, with the maintenance going up to compensate. Maybe the hanger and radar work at half efficiency until they're fixed, with a slower refueling and scans on the hour instead of half-hour respectively.
As far as I know, none of these would require different tiles, it could just activate functions that are already there. One thing I do see maybe being a problem is if the game can remove single use workshop projects once they're completed.