I suspect, given the geographical look of the region and its historical borders, that you'd have
1)A state astride the Nile (Egypt)
2)A Sunni Levantine state primarily using the Med for navigation (Greater Syria)
3)A Mountain state at the edge of Anatolia (probably Kurdistan)
4)A Shia Mesopotamian state at the Tigris and Euphrates - (this will still invite sectarian violence, but it's just not possible to make a Sunni state viable in Iraq under any borders)
5)A Hejazi state along the Red Sea (Hejaz)
6)Bedouin states in the Syrian desert and Arabian Peninsula
These should provide states which exert maximum control on their populations, and so have the resources/force necessary to challenge any ideological threats to their rule without requiring potentially destructive divide-and-rule tactics that most Arab states now use.
That said, I don't really agree that 'natural' states exist in the Middle East, at least not of the sort where a geographical majority identifies with a set of common symbols and history (beyond Islam, which is not exactly enthralled with the idea of individual states). Arab identity in post-WWI Middle East was centered around religion/sect, tribe, and city-vs-rural identities, not some geographical attachment. The intellectuals in Damascus, Baghdad and Cairo, those whom in Europe we'd expect to form nationalist narratives - they were concerned with Arabs as a whole, and really had more in common with each other than the peasant/Bedouin living 50 miles away.
Sykes-Picot of course drew artificial borders, but any other border arrangement save an Islamic/Arab socialist unity would have been just as artificial. Despite that, ME states have generally managed to cobble up some sort of 'national identity' pretty well: Iraq, Syria, Jordan, Palestine etc. have demonstrated their cohesiveness through fending off 'threats' like pan-Arab socialism, secession movements, and each other (notably Iran-Iraq, but note that Lebanon has not collapsed into Syria, nor has Palestine collapsed into Jordan).
I would argue that alternative identities such as Islam and ethnicity are successfully competing with the idea of 'the state' for public allegiance nowadays because state leaders have generally failed to deliver benefits to their countrymen. In such a view the question of whether the Sykes-Picot states are 'natural' is irrelevant.