For this a low power, low performance application.  My go-to microcontroller is the ATtiny84A:

• Wide input voltage range (no need for 3V3-LDO when powering by Li-Ion)
• Plenty of peripherals (I²C, SPI, timers,...)
• built-in EEPROM
• no UART (but SoftwareSerial possible)
• enough GPIO
• SOIC-package which is easy to hand-solder
• Arduino & PlatformIO support
• previous experience with AVR-family
• 100nA shutdown current