Standalone controller for ESP8266 project

Hi - newbie question here ....

I have a built a project using the NodeMCU (ESP8266) and would like to make a small number of units with a cheaper / standalone controller rather than using the whole NodeMCU IOT board.

Q1 - what are my options? My code uses 3 interrupts, so I don't think the Atmega328P is an option as I think there are only 2 interrupt pins?

Q2 - when I choose a controller, how do I flash it?