I think one of the reasons why we today seem to be confused about the ethnic and religious make-up of the Middle East and its borders (and the same goes for parts of Africa as well) and desperately look for answers to why this happened is our somewhat loaded view of an "orderly" region -- as you used the word yourself. We have this view of orderly Europe with its neat nation states but forget that it took a lot of time and blood to sort itself out like this. In some states one culture became the accepted one and was forced on the periphery from top down (like in France), some just separated somewhat peacefully (e.g. the Czechs and the Slovaks), some incredibly violently (i.e. former Yugoslavia), other regions took world wars that just relocated borders and populations (Central Eastern Europe). In the best case different communities found a modus vivendi in one state (e.g. in Spain or in Belgium) where the advantages of being together outweighed the disadvantages whatever they might perceived to be -- and even then this was not always a non-violent process by any means.

Nationalism is historically speaking a rather recent phenomenon and with it came the idea that people of a certain language, of a certain faith, or whatsoever ought to be together in their own state. To us, about 200-300 years into the "age of nationalism" as we might call it, the idea that a certain group has the right to its own state comes naturally, but the people of the past didn't think in these categories.

Regarding the specific case of the Middle East and the partition of the Ottoman Empire, yodatsracist wrote a wonderful post some weeks ago which might be of interest to you.

Yes and no. The exact nature of the breakup of the Ottoman Empire in the aftermath of WWI certainly contributed to the problems that we see in the Middle East today. In The Ottoman Peoples and the End of Empire, Justin McCarthy suggests that European Imperialism and the machinations of European states, more than anything else, led to the destruction of the Ottoman Empire and the subsequent destabilization of the region. But the increasing prominence of nationalism in the region was also destabilizing, and the various and competing claims of different ethnic minorities in the decades leading up to WWI, and in the course of the war, would have been hard to sort out had the Ottoman Empire not been carved up as the reward for the victors of WWI - namely Britain and France.

Still, it's hard to imagine a worse situation than that created by the manner in which the French and British (in particular) split up the Middle East. The immediate aftermath included the Turkish War of Independence, which led to the deaths of hundreds of thousands of Turks, Greeks and Armenians (and right after the demographic destruction of WWI). The long-term aftermath included the creation of borders and units of government basically out of thin air, which certainly exacerbated the problems of ethnic and sectarian conflict that probably would have been present to some degree no matter what. The Ottoman Empire had been very good at managing a multi-ethnic empire, but the rise of nationalism certainly posed a challenge, and the apparent acceptance of ethnic nationalism by the Young Turks who came into power shortly before the outbreak of WWI (part of the reason that the Armenian Genocide is considered a genocide) and subsequently by the Kemalists in Turkey suggests, to me, that the old mechanisms holding together the diverse groups within the Ottoman Empire were being rejected by the Empire's new leadership. This is getting a little too near historical "what-if" questions, though. Suffice it to say, there were some conflicts in the Middle East while the Ottoman Empire was still around that probably didn't have neat solutions, but the way that the victorious powers made conflicting promises and carved up the empire's remains definitely made things worse and influenced many of the problems that persist in the region today.

I think the Rome comparison is interesting, but I don't know enough about the disintegration of the Roman Empire to really do a good job answering that question. My basic feeling is that the two occurred in quite different contexts, and thus followed different courses, but hopefully someone else can talk more about Rome.