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Is there any reason not to use InnoDB by default?
I just noticed that $LJ::USE_INNODB isn't listed in etc/config*, doc/config*, or cgi-bin/ljdefaults.pl. Before I file a bug, a question: is there any reason why the default/initial/suggested value should remain to the current "don't use it"?

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They're similar, especially in the case of MariaDB, but the difference is that they're still independent projects and are gaining a lot of traction in the open source world. They're not Corporate Zomg Projects.
OTOH, MySQL will work for a long time to come I bet and it's so widely supported...