Are you going to publish this work for profit? If so, you would be best advised consulting a copyright lawyer, because it would be a tragic waste to invest all your time and effort into making a sellable product only to have WotC send you a Cease and Desist order.
I'm not a lawyer, but what I can tell you from what I've seen in other products is that a LOT of things can be changed, if you still want to be able to put the "d20" trademark on your product, but among the things you can't change under the d20 STL are the six ability scores, and the way experience and levelling is applied to a character (in fact, you can't even MENTION the latter). Under the OGL license, you cannot put the "d20" trademark on the product, but you can use ANY of the System Reference Document you wish, as little or as much as you want. You STILL in all cases have to put a PROPERLY written copy of the Open Gaming License in the product, crediting the section 15 in a proper fashion. the documentation at
www.wizards.com/d20 will have more info, including the things that CANNOT change. EVERYBODY who makes a d20 or OGL product should read and understand every word of those two licenses before publishing anything.
Also, I'll move this to the d20 Publishers forum, because someone there may have even more accurate information for you.
Good luck!