I use MySQL Workbench 5.2.38. and I have made an EER Diagram. But on export I got surprised with InnoDB as defined storage engine. Altering the table afterwards is not an option
Global preferences should be respected by default in the Workbench Model Editor. If not, you should file a bug about this issue.
However, here's another solution that I've tried and it worked:
Model --> Model Options...
Use Global Settings
checkbox at the bottom of the dialog that appeared.Model: MySQL
tab and select in the Default Storage Engine
combo box the storage engine you'd like to use.Once you do this the generated script will use the storage engine you selected.