New CLI migration tool is in CVS, I have searched through the docs, the InnoDB is already recommended. I think we do not need to change the docs because if the MyISAM is the default database engine, we actively search for InnoDB and use it unless admin specifies the MyISAM in dbobptions explicitly.
1/ old sites with at least one MyISAM table are warned on the admin/index.php page
2/ there are two tools for migration - the web UI for innodb only, the CLI script that handles any engine migration and list current engine for each table
3/ new installations ignore MyISAM as default DB and use INNODB or XtraDB instead
4/ when adding new tables during upgrade we always use "current" engine detected from the config table
5/ mysql transaction support detection is more intelligent now
6/ you can for override engine and transaction detection via dboptions - no queries used == better perf
7/ the recommendation is a lot less radical than in the patch above, feel free to tweak it as necessary
I hope this will make the transition away from MyISAM as painless as possible.
Thank you for the feedback and ideas!