When you try to Create Repository or Delete Repository from within Tools -> Repository Management, it seems safer (and maybe necessary for some versions?) to use a separate schema for migration repositories created by different versions of SQL Developer.
In order to see which SQL statement failed during a repository create or delete, look at your View -> Log -> Statements to see the most recent statement.
1 - why are you using 2.1 vs 18.3?
2 - there haven't been many changes in the MySQL support, but you would want a newer copy of SQLDev for things like 11g and 12/18c database support
i can think of no reason to use version 2.1 in other words