the rp2040w has wifi, micropython and a bunch of GPIO, all running at low hundreds of megs. Great for motor controllers and that sort of stuff. I use them a lot for the sort of things I would have used Pis for.
However thats because its python. If you want rust, or javascript, then the pi is probably still a good option (I know there are native ports, but they are not as common or easy. )
But if you want computer vision, or, can't be arsed with micro based programms, then pi is where its at.
The other type of application is home assistant. I have an N100 running HA in a VM. It would have been easier with all the home security stuff to have it running on a pi directly. (yes you can use esp32 as binary sensors, which is what I do, but its expensive to have things that aren't wifi.)
Another I have thought doing is ADS-B receiver mounted outside. It helps to put the receiver close to antenna so would put the SDR and Pi in enclosure, and power it from PoE. Microcontroller can't run the SDR. Micro PC is overkill and wouldn't work in enclosure. Doesn't use GPIO pins.
Linux would probably be very easy to built without needing firmware
I've also used GPIO on a Raspberry PI Zero W to build a Stratum 1 NTP server with nearly spooky accuracy with the PPS line.
Both things worked very well. They were compact, performant, used an inconsequential amount of power, and were very inexpensive.
And both things were very easy for me to implement, largely due to the tremendous amount of software available in the Linux-ey ecosystem.
If I were trying to bodge an MCU into performing these tasks without involving Linux, I'd probably have never gotten either of them done.