If you want to insist the empty 'set' is not a set, then you will have to modify restricted comprehension appropriately. And this seems to defeat your whole idea of rejecting "higher and higher order classes", because you are putting all other sets on a "higher order" than the empty set.
And if you're going to seek out a theory with a 'set of all sets', you're going to have to find a way out of all of the classical paradoxes, such as Russell's paradox, or Cantor's proof that there is no injective function from P(S) to S.
Incidentally, one method that people use if they really want to talk about universes as if they were sets is to invoke a large cardinal axiom, so that there exists some set
S such that the elements of
S (often called "small sets") form a model of ZFC. In this way, you can speak of the "large set of all small sets". e.g. see
http://en.wikipedia.org/wiki/Grothendieck_universe
If you're willing to go in another direction -- I believe that in constructivism, depending on what you meant by 'set', you can easily have a set of all sets. However, constructivism gives up Boolean logic. (I can't say much
intrinsically about constructivism, because I'm only really familiar with the perspective given by the theory of computation. i.e. studying Turing machines)