I'd love to see Reactor Incremental style mechanics implemented in more ways in more things. Being able to pop open the hood and apply critical thinking and puzzle solving to pieces and having the cost/output based around how good of a solution you came up with is so much nicer than arbitrary 'buy X things, each things does the same but costs more than the last. For the price of 100 things you can double the things thing-doing output.'

Also visual customization is fun. If it had a bit of a minecraft/terraria/lego vibe to it people would build all kinds of crazy stuff in their downtime. Especially if the shops and stuff were NPCs that needed to do certain tasks. So that way players would use the building mechanic to make a blacksmith shop and the engineering mechanic to make it efficient (managing heat input and output for the forge, forge start up times, electricity connections and use, material transportation both in and out of the building as well as between stations within the building, ect)

I guess my ideal game would be like Idle Blacksmith but each step in the process is a structure you build and add to a grid-map and slowly upgrade the pieces of to make better but also prototype new designs to make more efficient and decorate. And as you go new pieces that do different things become available. (Like a heat generator that only produces heat in one direction instead of every direction, or a device that automatically sorts items put into it into two outputs) And then I suppose it would get more complex, generating new and more kinds of resources used to upgrade things and ultimately having to have your resource refiners do different things using the same space to output both items in the desired ratios. And then for progression you'd start out manually carting items around and operating machines , then you'd get NPCs you could instruct to cart items around and specialized NPCs who would seek out and operate machines on their own (blacksmiths for example would gather the ore closest to the forge, smelt the ore, bring the ore to the anvil and create things out of it) and then more endgame stuff would involve more advanced versions of the pipes/conveyor belts used in the machines to move items around instead of NPCs, and phasing out NPCs with robots that would lack AI but be programmable and ultimately have better stats.

So the basic gist of the game is that you can do everything yourself, but if you're clever you can slowly automate every single thing in the game. I don't know what the 'win' condition would be or how it could be infinitely scaled, but with enough complexity it could easily be a game that takes months to complete. And that isn't bad.