The major problem is that a large part of your transistor characteristics are defined by the initial slab of silicon on which everything is built up. There are currently viable techniques to grow a pure bulk silicon layer on top of the silicon oxide layer which is used as the isolation between metal wires.
(And then there are, indeed, the other factors that Frank pointed out.)
So either you'll have to come up with something completely new, or you'll have to somehow glue 2 separately processed wafers together. Which is probably not what you had in mind...