Not a traditional urban-realism example, but my favorite flexible sim is the new Zelda game, Tears of the Kingdom. Right during the tutorial you're given powers to:
- Telekinetically lift, rotate, and glue together anything that is not alive or nailed down.
- Summon and activate small mechanisms (fans, self-spinning wheels, flamethrowers, hydrants, etc).
- Phase vertically through any ceiling, as long as it's not too far away. This includes mountains, floating platforms, and large enemies.
- Reverse the last ~30 seconds of any object's motion. A falling boulder flies back up, a floating plank goes against the current, a spinning wheel changes direction.
Then you get to apply these powers for transport, combat, and puzzles. And somehow it just works.
I found myself frequently wondering what is the canonical solution to a puzzle, because it sure as hell isn't what I just did. It's a brilliant game.