What if Windows crashes? It's better to attach a thermal sensor to the heatsink, I think.

RP2050 would work, as it also has the necessary built-in peripherals. ESP32 would add wifi and better ESPHome support. I suggest you stay away from the ESP8266, as it needs to do PWM in software and struggles with the 25kHz output frequency.

From my experience: ESP32/RP2040 work without additional circuitry which works with most fans, but for protection, you want to add level shifters. Not all fans pull up the PWM pin to 3.3V, the spec allows for 5V.

Shameless plug, hopefully this is allowed here.

I built something like that, that allows fan control via WiFi. First I built it only for myself, but since the spare boards from PCBA quickly sold, I decided to keep it stocked.

Short gist: 12V Input, ESP32S2, ESPHome-based. Has 4 PWM-fan outputs, onboard temperature & humidity sensor and Qwiic expansion port.

The ESPHome code & schematic is on Github: https://github.com/zeroflow/wifi-fancontroller

If you want one, it's available on Elecrow for $35,99: https://www.elecrow.com/wifi-fancontroller1.html

If you want to build it by yourself, the schematic is in the hardware folder. And if you don't want to use ESPHome - there is no firmware lock, you find the pin assignment on the product page and can write your own firmware if you so desire.