Hello!
Just to be sure about: Older MediaWiki installations (1.11, 1.15) show almost just MyISAM tables though InnoDB is always set in the LocalSettings.php; 1.19 installations show mixed, though MyISAM dominates (and InnoDB set in the LocalSettings.php); in contrary 1.22 shows just InnoDB tables. (All on MySQL, 5.0/5.1.)
So I think though InnoDB was always set MediaWiki used basically MyISAM tables, but changed this behaviour through the versions in direction to InnoDB. Is this right? (Did not find anything regarding this in the HISTORY files.)
Best regards
Jörg