There is significant portion of customers which are still using MyISAM when they come to us, so one of the big questions is when it is feasible to move to Innodb and when staying on MyISAM is preferred ?
I generally prefer to see Innodb as the main storage engine because it makes life much simpler in the end for most users - you do not get to deal with recovering tables on the crash or partially executed statements. Table locks is no more problem, hot backups are easy, though there are some important things which we have to consider on case by case basics before recommending the move.
Is MyISAM used as default or as a choice ? This is the most important question to ask upfront. Sometimes MyISAM is there just because it is default, in other cases this is deliberate choice with system being optimized to deal with MyISAM limits,
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