Well the database fields are completely different, you can have a look at the screenshot I took from phpmyadmin for Mys v1.4.0 dev for some insights. Note there will be even more tables to store some settings for certain features, although these can also appear as flat files in .xml format:
However, this does not mean upgrading database will not be possible. There will be mapping for old Mysidia database tables/fields to new Mysidia database tables/fields. It can be complex, but its doable and easily automated. I will release a beta version without upgrader at first prior to the official stable release, during this two weeks beta testing phase I will try to design an upgrader for database.