For one, Aegis is more well known. Aegis has 6k+ stars where FreeOTP+ has about 500. This doesn't mean it's better, just that people are more likely to recommend it.
Aegis also has more features, and can import from many different authenticator apps (though as many don't allow exports, this may require technical knowledge to get the database and feed it in). If you have root then Aegis can pull directly from the other apps.
Aegis claims they are better than FreeOTP because the encrypt passwords at rest.
One big difference is FreeOTP+ lets you not have to enter a pin/password to see the codes while Aegis you need to enter a pin, password, or biometric to see your codes.