The biggest change is that the Legend weapon, formerly always a sword for Paladin Cecil, is now exclusive equipment for whoever it is awarded to. So, if the main character becomes Porom when she receives KluYa's blessing, the weapon will become the Legend Staff, with the same stats and properties as the Legend Sword, but only Porom (and not Rosa or Cecil) can equip it. This change propagates to the Excalbur, should you obtain it. Also, the randomizer logic now demands that one, and only one, Rat Tail will get placed somewhere in the world, rather than just usually happening to produce one.
In other news, sleeping in the Inn will now be less time consuming if you are using the shortened cutscenes option. The poor receptionist desk guy will see you collapse as soon as you pay your money, rather than traveling to the beds.
There are a number of other bug fixes, too - for example, it turns out that v1.08 really doesn't like it if you try to make multiple seeds that use the Randomized Names option with the same instance of the program, and no longer will a seed with Golbez not in your party necessarily have Golbez as the villain.