Wrong: https://apps.apple.com/us/app/japantaxi/id481647073
Need to communicate destination.
Not with the app.
Primarily use cash
Wrong, you can pay by many means, including the IC card, this is a good option and can be used with Apple wallet, super convenient.
Expensive
Compared to what?
Paper receipts
Not when using the app, you can just say you don't want a receipt.
No real-time status tracking
Wrong, the app does this too.
Hard to get back lost items
Call taxi company, get it back? Tokyo taxi drivers usually inspect the taxi before you get out too, I notice they do this every time I get a cab.
Another benefit IMO is there are cabs driving around everywhere, you don't have to hail and wait for a cab, if it starts raining, you can just jump into a cab usually in under a minute.
No apps, need to communicate destination (possibly in a foreign language), primarily use cash, expensive, paper receipts, no real-time status/tracking, hard to get back lost items, etc. They might be cleaner and quieter but those are minor details.