The conventional wisdom regarding InnoDB versus MyISAM is that InnoDB is faster in some contexts, but MyISAM is generally faster, particularly in large loads. However, we ran an experiment in which a large bulk load of a mysqldump output file, which is basically plain SQL consisting of some CREATE TABLE and CREATE INDEX statements, and a whole lot of huge INSERT statements, in which InnoDB was the clear winner over MyISAM.
We have a medium-sized database that we have to load every month or so. When loaded, the database is about 6GB in MyISAM, and about 11G in InnoDB, and has a couple hundred million smallish records. The MySQL dump file itself is about 5.6G, and had "ENGINE=MyISAM" in its CREATE TABLE statements that we "sed" substituted to "ENGINE=InnoDB" to do the InnoDB test.
Load time with ENGINE=MyISAM: 203 minutes (3 hours 23 minutes)
Load time with ENGINE=InnoDB: 40 minutes
My guess is that the performance difference is due to the fact that these tables have lots of indexes. Every table has a PRIMARY KEY, and at least one secondary index. InnoDB is generally better at large index loads than MyISAM in our experience, so the extra time MyISAM spends doing index population swamps its advantage in simple load time to the base table storage.
Given our experimental results, we'll now use InnoDB for this table.