Naturally, you are able to choose exactly what is randomized in your particular ROM.

The moves taught by move tutors, for games within which they are significant enough.The names of trainers & the classes they belong in.The 'static' Pokemon which you either are given, fight on the overworld, or are sold.The ability of each Pokemon to learn each TM or HM move.The contents of each TM which can be taught to Pokemon to give them additional moves (HM moves are not changed to make sure you can still beat the game).The moves that Pokemon learn by gaining levels.The abilities of each Pokemon, in games where they exist.The base stats which define the potential of each Pokemon.

The Pokemon that Trainers use against you.

The Wild Pokemon you encounter in grass, caves and other places.

In the same vein as previously released randomizers, it provides a customized gameplay experience by allowing you to randomize many things: The Universal Pokemon Randomizer is a program which will give you a new experience playing Pokemon games.

Moemon randomizer