A CR2032 battery will last for more than 10 years. Super capacitor costs more. Any particular reason to consider using super cap?
A warning; I have experience with 32F407 and haven't checked if the same applies to your 429... Check if there is a PDR_ON on the pinout and tie it to Vss. With lower pin count devices (64, 100) this pin is tied to Vss internally, but on higher pin count devices (144, 176) you have to connect it to a positive or negative potential. If this pin is not tied to Vss you will drain the battery in a week. Check the datasheet for more.
Edit: PDR_ON should be tied to Vdd, not Vss. On the lower pin count devices the PDR_ON is not connected to Vss internally. Read further down.