I've had a few thoughts about a lot of these for a lot of years now:
Electricity
I'd personally prefer if electricity had only a maximum amount it could transfer on a given energynet, say, 1MW or 10MW or whatever for the lowest tier, however you could have different 'tiers' of energynets, such as the small/medium power poles are one, the long distance power poles are another (probably a third somewhere), and they don't connect. Buildings would only connect to a single tier of energynet to draw electricity, so low level things would connect to small/medium poles, higher tier the larger poles, etc...
To connect the tiers you'd use transformers. This way you'd have, say, tier 2 poles branching through a base with little tier 1 poles via transformers on those to go out to the various branches. Tier 3 would be for running huge amounts of power, might even need to run multiple energynets from excessively large nuclear reactors.
Nothing like poles catching fire with too much electricity or so, just like when you don't have enough power to supply the machines then the machines slow down as normal. This would be cheap to calculate and add an interesting thing to deal with in the game, plus it would help keep the individual energynets small if that's useful in any way (easier to distribute and average the electricity to the entities perhaps?).
Water
Water could work the same way, low 'flowrate' pipes as tier 1, it's still instant transport, just only a small amount per tick, they can connect via pumps or valves or something to higher pressured larger pipes that have higher 'flowrates' and so forth, essentially working the same way as electricity above. Offshore Pumps really shouldn't be magical water-generating things, should take electricity or mechanical energy of some form.
Heat
This seems expensive to calculate, so wonder how this could be helped with that style as well...
Mechanical
Perhaps for a Factorio 2 or something, but a mechanical system, rotation or so, essentially transferred like the above styles, gears and all to buildings that need it. Electricity is not the most efficient form of storing energy, in real life there is often mechanical energy transferred around via axles/gears/etc... to various machines that just use it straight, no electricity involved or needed. I still find this odd that it's missing honestly. Even transferring steam pressure around is not uncommon in the single-building scale in real life.
Item Transport
I like that belts are low tier, but they are 'too' low and take no electricity/mechanical_power to run (like 'enough' mechanical energy should be able to turn a whole 'touching' set of belt for example). A lower tier could be little wheeled drones perhaps, slow, move along paths , etc... Should be fairly efficient to calculate with hardcoded path objects to move along.
A medium/high tier item transport to replace bots I'd think should pneumatic tubes, powered via a pressurized system, and with that constant energy drain they can move items (transporting essentially) inside the enclosed tube 'network' to filtered areas. Think of them like using the logistics chests, but connect pneumatic tubes to them instead, they request certain items that are fullfilled elsewhere on the network. Could of course have tiers and throughput of this as well so for high-load items it would not be able to sustain the throughput needed as well. Perhaps make it so you have to load up canisters with a few dozens stacks before loading 'that' into the network and use tags for matching where things should go. Pressurization could only work on smaller scales so no long distance. Should be much cheaper to calculate than lines of belts and so forth (would be interesting if could run into buildings via a filter or so as well?)
Inserters I don't think should 'chase' items, rather they should just move back to the belt and 'wait' for an item to cross them on either path, then pick that up. That gets rid of the chasing, simplifies the code a lot, doesn't "transport" an item that has already passed it into it, etc... Might be useful to add an end-belt though that stops halfway down the tile perhaps, though meh on that, can just run the belt 'into' the inserter if its at the end then, the inserter could grab from that end part then instead of the middle.
Bots I still think should exist as they are, useful for the extreme high throughput needed for some setups that pneumatic tubes don't have the throughput for.
Enemies
I like that clearing the pollution cloud makes you safe for a bit, though I definitely think that biters should expand nests a *LOT* faster when there is a lot of them. I currently play with biter expansion set at near the minimum. Rampant also works very well for testing where a base is weak. It looks like it works by having the bugs go from chunk to chunk, testing what's safe, and if a chunk is safe they run along it fast, probing around my walls until they find a weak spot where they die the slowest, always probing and updating. I really like that mod a lot.
Miners
Yeah Miners shouldn't output to a belt, should just hold an inventory until full, inserters should pull out.
Although I do really like the thoughts of belts going into/out-of buildings, inserters are a lot more flexible though.
Boilers
Boilers I like having a 'pass-through' for the water, unsure how it could be made more explicit. Honestly I liked the old style ones a bit more, could heat up a whole line of water to pass into a whole line of engines, it was very logical. Though if water could still turn into steam when it reaches 100C and pass through then that would be very nice. Engines taking in water should eat the water but make a pittance for energy, barely scaled with the temp. The current style of 2 engines per boiler off to the side is pleasing to look at it, but the old way made more 'sense'.
Items & Construction
Should definitely have mass and size. Carrying an entire base in my inventory just seems so so very wrong.
Even producing a building, say an Assembler, seems odd, rather you should put down a kind of 'blueprint' for a building somewhere, then fill it up with the parts it needs, once filled up then 'build' it akin to how repairing works (and all of this could be done by construction bots) until it is complete. Graphically the building could be an empty marked off area for when first placed, has some generic 'things' inside that area when filling it up but not full, and a full area when filled (3 states), then 'building' it could go through a few graphical states as well until the building is completed.
As a Mod for now someone could even make it so when someone/something places a building then it starts at 1hp and disabled, and has to be repaired back up to full health before it becomes enabled and works. On the whole Total Annihilation vein of things, one of the most popular mods (Balanced Annihilation, among others) there is a building/repairing tower that can help construct with the builders in a large radius, they were very useful especially as they could help buildings construct other things, like vehicles.
On the things of vehicles, they could be just like building a building (except on the 'pad' next to a building perhaps, initiated by the building itself) that then has to be filled with things (either by the building's inventory like a recipe, or by manually placing things in it), then constructed, of which such construction turrets could help with as well.
Hotkeys
I quite like the whole variety of hotkeys you can place, though I don't think many should have hotkeys set by default. The hotkey for a 'tool' should also show on its popup, and should also be settable on it as well without needing to open the hotkey screen.