I am about to convert a database from MyISAM to InnoDB and I was advised by someone that there might be 'structural issues' to resolve first. However that was all they said! Do you know what kind to structural issues could prevent a database from being converted from MyISAM to InnoDB. I am aware that InnDB doesn't support fulltext searches before 5.6 so fulltext fields could be a 'structural' issue in one sense, but I am presuming any schema can be converted from MyISAM to InnoDB.
Creating a new table that uses InnoDB and copying is so that you won't suffer any data loss if the conversion goes wrong. I believe that you don't even have to export the data if the table is in the same database. Read the info on this page: http://dev.mysql.com/doc/refman/5.6/en/ansi-diff-select-into-table.html It looks like you can do the whole operation in one line of SQL. If you have created the new table, you case use:
Creating a new table protects you from conversion corrupting data. It avoids dealing with issues of conversion in the original table by allowing you the opportunity to redesign your intended schema in the new engine. Because the purposes and features of the engine are different, it could alter the design. Therefore, it is like migrating from one database to another. You can use tools to automate the migration, but often the headache of resolving the issues caused by the automation are worse than the tedious nature of recreating system from scratch and importing data if that makes sense.