Minnflier has made this suggestion many times. I know it will work. Just give the ailerons a little more throw. I have thought some too. You want to do some 3-D eventually. I think your idea of adding some depth to the ailerons may be good for you. most people would not notice it. You may. I won't really hurt. If you find it too much you can always dial back the throws. I would also suggest you take all or almost all of the dihedral from the wing. It will help some there too. Good luck with your project. BTW you will be surprized how much authority those 1/3 length flaps will have. Half would be serious overkill. And cut back the aileron performance too much.

Mark Shuman