I know that you are working on the Structure Sync Tool right now.
Just as the 'copy table to other host' does allready I propose an semi-automatic 'stripdown' facility with the Structure sync tool. Let me explain:
You use the tool for comparing a MySQL 5.1 database with a previous version. The 5.1 database may contain PARTITIONS, OBJECTS, ('modern-style') CHARSET/COLLATON information.
Before pressing the 'Compare now' button there could be a 'strip down to target format' button. If for instance target is a 4.1 database PARTITIONS and OBJECTS should be removed, however CHARSET/COLLATON information should not.
Part of the code to use for this must be in the code of 'copy table to other host' allready, and the issue with 5.1 >> 4.1,5.0 should be solved anyway!