I know the basic differences between the MyISAM and InnoDB engines. In MySQL 5.6 beta, InnoDB will support fulltext search. But, I wonder why previous versions of InnobDB didn't support FTS? My guess is because table storage format or the way that data is indexed. Sorry for my ignorance.
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I am sure one of the biggest gotchas that developers worried about was making FULLTEXT Searching (FTS) work in harmony with Transactions. This is especially needed since the tokenization for inserted strings is performed only at commit time, so a full-text search does not see the uncommitted data.
An alternative is to use two tables synchronized with each other with InnoDB and MyISAM. In the second table we could look through a function and return the data from the first table. There is an example here