Migrations stay pretty small. Most of them just add a column or index. We also have to make sure tables aren't too hot to migrate. See a previous post for more on that: http://githubengineering.com/using-mysql-performance-schema-...
It's also really important that migrations don't affect the running app code. New columns shouldn't be used yet. Removed columns or tables need to have all references removed first before running the migration. We confirm this with a deprecation helper that sends metrics to Graphite.
That's about all I can answer from the app side :)