Huge amount of text. Do you have any particular question or a part that you need help with?
You said it's your first project so don't you think you are trying to do a bit too much with character customization, three tiers of gameplay, classes and skills?
I guess I'm not looking for any particular answers. Really, all I'm looking for is advice on how I should go about making the game, hints and pitfalls to avoid, and maybe some games that are similar to get ideas from.