Development of a more structured version is in progress. I just committed a set of changes to the repository that changes the current, rather monolithic, single-class design to what will be the first step of a more modular one.
Currently the generation of ALTER TABLE statements has been removed and the output format of the analysis is slightly different. But that is mere cosmetic.
What is much more important is that now the gathering of database schema information is based on a pluggable system, designed around an interface called IndexDescriptorProvider. Up to now I have just ported the MySQL 4 stuff that was already in the first version to this new architecture. Please feel free to have a look at it and tell me what you think.
Next thing I'll do is implement a provider based on the INFORMATION_SCHEMA database available in MySQL 5.x to see if I missed anything.
Go to http://mysql-index-analyzer.blogspot.com for details.