Story story story! I'm still learning this lesson as I go along. Let me explain why it is so important to get that first. It doesn't matter if your "story" is an actual story game or just a mindless beat em up. You gotta have some sort of plan, a world, names, labels, titles, whatever. Why? Well...:
You will build your characters, as the story grows you will add more characters. Once you have a good solid grasp on what the story is, you can make a much better guess at how many characters there are supposed to be, so you can set up a proper limit for yourself without falling short.
You can add titles to these characters, classes, give a rough draft of each characters personality and use that to build on what sort of classes you want, what sort of skills they should have. If you're still following me, that's already three tabs you can get moving right: Actors, Classes, Skills.
The same goes for the enemies. What are the enemies of the world? What are they going to do? Back to skills again, but this time you are using enemies to help you build up the skill database. And your enemies will be build from whatever world you have built when creating your...story!
Create some events, create some actors, create a world. Pick a starting point, whatever comes easiest to flesh out for you and build on that. Then jump around and see what else materializes from what you have started. You will jump around a lot but the best place to start is probably the story/world.
All of your skills, classes, they're all going to be dictated by your world. Is it magic based? Is it techno based?
Don't rush ahead too far until you have set up your skills. But be sure to get the actors and enemies out. This way, when you do start on skills, you know where they go, you know how many you should have, etc. The Skills tab might be one of the more trickier ones to set up right because that is where all of the character actions will be dictated. From attacks, to behind the scene commands to special strikes, etc, etc.