Hard to see where the solution is here about avoiding military coups. Under the emperors of Rome east and west it was the army supporting a usurper. In medieval times a noble who thought he should be king. In the last 100 years its been back to a military putting an officer or demagogue in charge. The countries in our age that seem to work the best against that is democracies that have a large enough base of population that have a stake in the status quo to make sure the military follows the will of the majority and a tradition to do so. The problem Romulus has is there is never been system before him, that has solved that issue. He does seem to have some ideas that way, will see how it goes.
It's true that usurpers, rebellions, and other examples of destabilization have played large parts in destroying empires from within, but it's not the whole picture. Throughout history there have been countries that went through civil wars, uprisings, and so on without being utterly destroyed in the process. In the case of the Roman Empire, it ultimately survived numerous domestic conflicts throughout much of its own history; its western half being gradually torn apart after decades of civil wars, economic depression, political destabilization, and etc. At this point I think the WRE (compared to where it was in AD 475) has a stronger chance of surviving after Romulus Augustus' reign, at least in the immediate future, while the potential for civil war threatens the Pannonian dynasty more than the Empire itself. In some cases the conflict of civil war represents a violent change in government, which is less severe than the fragmentation or destruction of the entire polity. If it's a matter of the WRE's survival, I'd say they're in the clear, at least for the time being (again, compared to where they stood at the beginning of Romulus Augustus' reign). The Pannonian dynasty's fate is not as secure, however, because of the virtually unceasing threat of coups and civil wars, but even their possible downfall in the future is not necessarily interconnected with the fate of the western Empire.
The possibility of a Slavic Mesopotamia. Once they settle in an area its hard to take them out. Would it ring true as well in Mesopotamia?
Slavic, Germanic, Sarmatian... If the Empire prevails and implants its foreign allied armies into Mesopotamia/western Persia, I imagine that the region will initially start out as a mix of ethnically diverse petty kingdoms as opposed to being dominated by any single ethnic group from the start. Once they've permanently settled into their new homelands over the course of a few generations, I don't think they'll be easily moved. There are exceptions of course, like the compulsion to seek a new homeland, forced expulsion by a greater adversary, and so on. Anyway, once settled they'll gradually work their way up to things like consolidation or expansion, making alliances and enemies, integrating with the locals to greater or lesser extents--aside from some differences here and there, I think the overall process could reflect the settlement of the Germanic peoples in the former WRE to some extent.
And what of the Balkans? Given the Slavic exodus from that part of the world, would future nations there be Pannonia, Illyria and Moesia? Could they be as established as Spain and France? Would we be able to see Balkan Romance language flourishing there?
At this time, the Slavs hadn't poured into the Balkans like they did IOTL; the ERE still retains dominance over the European lands south of the lower Danube River, where some of the southern Slavic tribes are concentrated. The Slavs as a whole are not a united people, but rather various tribes that the Romans identify by a blanket term (similar to "Germanic" for example). So while there could be Slavs settled in Mesopotamia, it won't be all of them. There will still be Slavs in northeastern Europe, some or many of which could still end up migrating into other territories or even Roman lands. Pannonia is currently dominated by the Lombards ITTL. Most of Illyria remains under WRE control as the province of Dalmatia, and Moesia is still within the ERE--albeit with some degree of a barbarian presence (most likely foederati, which the ERE did have but not to the same extent as the WRE).
As for the future of these three regions, I'm really not sure yet but it will depend on how the future plays out after Romulus Augustus' death--a future which will be illuminated in TTL's epilogue part. Whatever languages emerge in the Balkans and other Roman territories as a result of this alternate timeline, I think they would be influenced to some extent by the current (as in "current" in this time period/6th century AD) versions of Latin and Greek, the two main languages of the Roman Empire. In the case of the Balkans, I would think that Greek would have a stronger linguistic influence, given that it is the primary language of the ERE, although Latin still remains the official language of the Imperial Court, administration, and military for now.