Many of these have been mentioned before, but I thought I’d aggregate the little quality-of-life issues and things that bug me when the city scales large (>4000 people or so). I’m not going to talk about fps and performance - that is what it is.
- Upkeep - at some point scaling on large maps just breaks. Currently, I have allocated 1000 builders, of which only ~350 are in use at any given time, and I have plenty of every material, plenty of laborers, etc. Yet I need to manually mark anywhere from 2-10 buildings every year for prioritized upkeep. I don’t know if it’s the distance - many of them are farther from the city, so maybe builders just give up - but there’s no reason the resources I have access to at this point can’t keep up with maintenance.
- Exposure - a varying number of villagers die of exposure every year, often in large numbers, and while walking past well-stocked temporary shelters or houses. Sometimes it’s just a few - sometimes it’s dozens! Maybe this is a deliberate mechanic, but it’s still annoying when I’m watching a villager freeze to death while walking right by shelters with plenty of room and supplies.
- “Upgrade all” and "Repair all." On one of my PCs I still use MelonLoader for these mods, as otherwise it is extremely tedious to upgrade (or in the case of a bad raid, fix) potentially 100s of buildings. This is a quality of life issue - some power tools to manage this would be helpful.
- Drag-to-place more building types. Fences and walls and roads of course this works well, but this ability would be very useful for many landscaping buildings - for instance click by click placing small plazas under a long road is very tedious. Same with parks, shrubs, trees, etc etc etc. Honestly, I would like this for shelters as well, althoug that’s a bit less important.
Attack Move . This disappeared somewhere along the way and it would be useful to bring it back. There are two workarounds - 1) is to place flags from the barracks, although that is tedious and needs to be done barracks by barracks, and 2) is to set a destination point for the troops, and while they are moving tell them to attack the nearest bandit - once he’s dead they’ll attack the rest on the way to wherever you told them to move. But I’d much rather just be able to select all of my cavalry and say “kill anyone you find on the way to this spot.” Related - if I use workaround #2, then unequipped soldiers will happily jog out to wherever I pointed them instead of equipping themselves. I guess sometimes this is useful, but mostly it just results in more dead soldiers.
Maintaining stock levels - this one is lower priority for me, but it would be nice in the late game to just tell the market to maintain levels, or auto-purchase (or sell) certain commodities whenever is possible. I run into two categories of issues here - 1) local production can’t keep up with needs, so I have to check every single trader and buy everything they have. Stone, for instance, is hard - even with maxed out deep quarries on the entire map, I can’t always keep up with stone needs, so need to buy from traders. That might be a game mechanic we want to keep, but it feels annoying when I’m drowning in gold. 2) in the late game, as fps drops into the single digits, I often just leave the game running in the background. There’s no point in me staring at the screen when it takes 30-60 minutes per year. So this means I miss the traders, and I run out of things like spice that only show up ever so rarely, and then my economy is off. Maybe this is a Tier 3 Market capability?
Harvesting Caps - 50,000 flax filling up all my storehouses is just too much flax. I’d rather let it rot in the field and let the farmers go harvest honey or make farmer babies or something. Obviously this can be controlled by setting caps at every individual warehouse, or replacing the flax crops with other crops - but there’s often good reasons not to do that (e.g. running out of flax is also bad)
Challenging the warlords - OK so this is more just for funsies, but I just thought of it. I enjoy the 1000+ marauder attacks that occasionally show up in the late game. I’d love to be able to send a diplomat to flash his bare bottom at the warlord the next valley over and taunt him to attack, just to spice things up occasionally. In the late game common raids pose no threat to the city, but marauding armies that I choose not to pay off tend to do some damage - in lost people if nothing else.
That’s it! I’m constantly surprised how much I just want to keep my cities going well past the point that there’s much expansion possible - these tweaks (plus figuring out how to get good performance at 5000+ pop 
) would go a long ways towards helping!
I’ll add to this thread as other late-game requests or quality of life issues occur to me.