Hi Alexander!
As you have probably noticed, phpMyAdmin 2.6.2 at its current state should be able to live with withs, which basically means that we still treat them as tables, but they don't break our interface anymore.
That's great news. In fact, what you implemented and talk about is exactly what I thought it could be like when we met at the last years PHP conference. Shame though I didn't have time to help you on this.
Anyways, your proposal to let the views be based on our display results is very handy and intuitive behavior. Combining/Replacing views with the bookmark system also sounds both workable and intuitive.
Bottom line is: The way you outlined it, is the way to go.
I would very much like to offer help on this issue. I should also be able to get into our current codebase in the next couple of weeks, and be of use again. My other hobby-project has come to a quite stable point for now, and I also need another project for change to dedicate work again for. What I mean is: I hope to be able to help you, but I can't promise. :-))
Great work until now, I just want to add.
Regards, Garvin