I have implemented a very small - and unobtrusive - change to Doctrine_Migration_Base that enables users to set application-level default table options for Doctrine_Migration_Base::createTable().
I implemented this change some time ago in a custom migration class. I wanted my migrations to always create INNODB and UTF-8-ready tables without having to always specify options. I blogged about it and others were interested.
In your boot script - for example - set default table options like:
'type' => 'INNODB',
'charset' => 'utf8',
'collate' => 'utf8_unicode_ci',
The enclosed patch, which includes tests, was created against 1.2 r6535.