Having to babysit your cemeteries and garbage dumps. You can close a cemetery to new plots but still leave it running. The game treats them like a backed up toilet. Similarly you should be able to make deals for your garbage. Like auto export it to another city, or auto empty it out to the burner buildings. No need to babysit.
The commercial and industry buildings popping up randomly and not being things that actually need to be there. Like when your new starter city has a single row of petfood stores for your entire commercial. I like the idea that my town is just a road out in the middle of nowhere, 100 miles from anywhere, and it's just a block of houses and 3 pet food stores.
There should have been an intelligence to what buildings spawned, based on a bunch of criteria like what needs have to be met, how many similar businesses of that type are nearby, and what street type they are zoned off of AND where in that street. Like gas stations are usually on the corner of a busy street, but they aren't likely to spawn on a small street surrounded by residential. That's a for a corner store or a coffee shop or something. It's very unlikely to spawn a gas station on the opposite corner of another gas station.
So there are priorities. When you start your new city you need the essentials.
High priority: Gas station, Grocery Store, Pharmacy, Clothing store, furniture store, plumbing and things of that nature
Medium priority: Corner stores, bars restaurants, entertainment, recreation, hair salon,
Lowest : Any kind Specialty retail, like pet supplies, cultural merchandise, souvenir shops, flower shop
So when a commercial building goes to spawn, it consults a chart and looks at the surrounding areas to make an intelligent decision. Are you on the corner of a wide road? Do you need gas/groceries etc... Spawn as needed. These places also don't fail unless competition spawns in.
Do you have room for 3 commercial zones in the middle of this residential neighbourhood, and your "must haves" are already met? What's quiet? You get a coffee shop, a flower shop, and cultural clothing store.
Is this a tourist area? Are there other souvenir shops nearby? Is the market oversaturated? No? Here you go. After that it's recreational and bars/restaurants. Maybe high end clothing.
Obviously you don't spawn a hair salon or a bridal/tuxedeo shop on the corner of the industrial block. It's just workers coming and going. You need places to eat lunch. A work clothes store. Maybe some hardware stores and equipment rentals. Contractors. Repair shops.
I think I made my point. Instead of this we just get random businesses pulled out of a hat that rarely fit their surroundings.