With the latest support for the MyISAM-Engine merging this pull request would save some trouble.
Background/Steps to reproduce:
If you have 2 entities with guid/uuid as primary key, @ManyToMany/@JoinTable fails on MyISAM, because it would create a jointable with 2 VARCHAR(255) columns and would apply a combined primary key on these two columns. But MyISAM doesn't support keys longer than 1000 bytes so you can't create the jointable.
The maximum key length is 1000 bytes. This can also be changed by changing the source and recompiling. For the case of a key longer than 250 bytes, a larger key block size than the default of 1024 bytes is used.
In my opinion this isn't just a "minor" issue but a major because some people can't run on MySQL with InnoDB for some reason.