This doesn't really answer your question. But I think you might find these comments interesting (even though I might not be saying anything you don't know).

By a theorem of Mazur-Ogus (Katz' conjecture) the $m$-dimensional Newton polygon of a variety lies above or is equal to its $m$-dimensional Hodge polygon.

A variety is ordinary if these polygons are equal (for all $m$).

For abelian varieties the $m=1$ case suffices and you see that an abelian variety is ordinary iff it is ordinary in the usual sense.

By a theorem of Grothendieck-Katz most varieties are ordinary. This is stated more precisely also in Illusie's paper you mention.

You should take a look at Mazur's beautiful paper on Katz' conjecture.

http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.bams/1183533965

Let me also talk about another nice subject which has to do with Newton polygons and supersingular varieties. Namely, "constructing" varieties with given Newton polygon.

If you stick to the case of curves there are many open questions (to my knowledge). For example, Mazur asks in *loc. cit.* (page 659) if all five different possible Newton polygons arising from a smooth projective curve of genus $3$ allowed by the restraint of Poincaré duality really arise from some curve or not. I don't know if this question has been answered by now (and let me add that it might actually be answered by now).

I can't really tell you anything else on supersingular varieties. It does seem to be a nice sport to look at "strata" in the moduli spaces of abelian varieties (=Shimura varieties). For example, every "symmetric" Newton polygon arises from an abelian variety (and the Newton polygon of an abelian variety is symmetric). See http://arxiv.org/abs/math/0007201 for even more beautiful statements.

For "strata" of Shimura varieties see

http://arxiv.org/abs/1011.3230 (Wedhorn-Viehmann)
http://arxiv.org/abs/1111.6830 (Kret)

These have to do with showing existence of abelian varieties with certain Newton polygons.

So the moral of the story is that it's already pretty difficult to prove that certain polygons arise from geometric objects, e.g., the case of the genus $3$ curves and the Shimura variety business.