I can't find it right now, but I do recall a designer describing their vision of a 5e group as a bare-bones Fighter with just Abilities, BAB, Saves, and Equipment playing in the same group as a Fighter with all that + Feats, Skills, Combat Maneuvers, etc. I'll keep looking for it.
Zack S. (who was hired by WotC though to what end he really hasn't said) postulated on such a system for his Type V posts (google them if you want, his site is usually NSFW). And either he or Jeff Rients I believe actually sat down and ran a game session with each player using a different rules system (some not even D&D) and stated that with the right DM tools and a bit of tweaking, it actually could be quite doable.

That said, I can think of a couple of ways to make it work. Building off the posts from Zack, you essentially want to build a system where the mechanically simple classes get a pretty standard flat bonus progression. For the complex classes, they get the better options at the expense of that progression. For example if a basic fighter gets a + to HP, BAB and Saves every level, a "complex" fighter might trade away one or more of those pluses to instead gain access to powers.

Another option would be to concede what early D&D recognized long ago, which was more powerful classes should advance slower. Give each class their own experience progression and have the simpler classes level faster than the complex classes. Heck if you do it right, that makes having the simple / medium / complex classes built into the book really easy because you can have different tiers of classes to group together (and add or remove as modules) and you don't necessarily have to worry that a level 10 basic fighter and a level 10 complex fighter are of equal power because they shouldn't be. Perhaps a level 5 complex fighter should be able to hold their own in battles that would take a level 8 or 9 simple fighter, and that's perfectly OK as long as it's given up front that comparing levels across classes and tiers is not possible, and that you should rather compare total XP values to get an idea of the relative powers.