Complex question. I would start by debating the implication that the Romans "lacked the ability" to conquer anything in particular. Rather, they were limited by distance and logistical practicalities in their ability to carry out difficult and extended campaigns such a distance from their core territory. Caesar's campaign in Gaul is an excellent example of a prolonged campaign (8 years) in which the Romans kept a very significant army in the field (80,000+) and routinely defeated large armies of slightly smaller, equal or much larger size (totaling hundreds of thousands) at least once a year, while maintaining control of a extensive, often hostile territory populated by a large number of capable warriors. The first two Punic Wars were even greater in scale, far beyond anything Alexander the Great would have thought possible. However, the conquests of Alexander the Great were a product of a certain place and time, and therein lie the differences.

Secondly, there is a significant difference between the armies of the Hellenistic period, capable as they were, and the army of Philip II/Alexander the Great (it was almost the same army). Alexander’s army was perhaps the finest Macedonian-style army ever to campaign (see Lloyd 175, 194). The Macedonian and Hellenistic armies that Rome fought over a century later were, in my view, only distantly related in flexibility and effectiveness to Alexander’s army. Regarding tactics, we should also observe the logistical challenges of campaigning in the East at the best of times, let alone operating from a territory as extensive as Rome’s was at the height of the Republic. The course of Alexander’s campaign was dictated very closely by logistical concerns. Alexander was forced to operate very quickly and with his movements sticking to areas where his army could be supplied (Engels 23, 121-2). Rome’s operations by contrast tended to be more measured but also far slower on the grand scale of things (Goldsworthy 104), but perhaps due to this care Rome’s conquests tended to be longer lasting. Rome’s logistical arrangements were far better suited to long-lasting conquests than anything Alexander could realistically have arranged (Roth 332). I would probably suggest that the battles won by Alexander could easily have been won by good Roman armies too: Alexander struck at a good time and won major tactical victories, which caused the fragile Achaemenid Empire to fall apart almost of its own accord. But this leads into my next point, in which Alexander’s conquests were not particularly enduring.

And so thirdly, we should note that Alexander’s conquests were militarily, politically and culturally extremely significant events in the East, they were not enduring in any ‘centrally governed’ sense and so are not really the same as Rome’s more permanent conquests. Alexander’s empire fell apart into rival factions immediately following his death, coalescing into a series of Successor Kingdoms in an end-result that is more similar to the fracturing of the Roman Empire into several smaller empires during the Crisis of the Third Century than any of Rome’s strategic operations during the Republic.

Regarding the Seleucids and Pontus, while they were great powers, Rome disposed of both of them handily. Pontus at the height of its power under Mithridates VI was utterly sundered and subjected to Rome as a result of the Mithridatic Wars, the successful completion of which was hindered more by political infighting in Rome than any real challenge to Rome on the battlefield. The greatly-feared Seleucids under Antiochus the Great were reduced almost overnight to a subject of Roman hegemony as a result of the Battle of Magnesia. The totality of Seleucid humiliation is evident by the story in which Antiochus IV, attempting to invade Ptolemiac Egypt with his entire army, was turned back by a single senator, Gaius Popillius Laenas, who with no army at his back ordered Antiochus to turn back, which he duly did for fear of war with Rome.

Overall, I wouldn’t say Rome lacked “the ability” at the height of its expansionism to conquer any contemporary civilisation, geographical and logistical realities notwithstanding. Rome’s distance from the Middle East, and far greater strategic priorities than further, quite impractical, expansion eastwards, made it extremely difficult and also undesirable to carry on any Alexander the Great-style ‘lightning’ campaigns in the East. Certainly the Romans carried on successful campaigns in Parthian and Sassanid territory in later centuries, but in the Republic Rome had far greater fish to fry: they were only just beginning to encounter the Persians and figure out what their strategy should be in the East. They were not half as familiar with the area as the fourth century BC Macedonians were. They were quite busy putting down rebellions in Iberia and Africa, knocking over Hellenistic dynasties, dealing with civil strife and fighting Gauls and Germans. That said, in a purely tactical and operational sense, Alexander the Great’s conquest of Persia is (as it was considered by the Romans) perhaps one of the most impressive military campaigns of all time, and he deserves credit for not only his tactical ability but also his remarkable foresight and planning ability in executing a difficult campaign, one that he had been thinking about since his childhood. In the medium-term however, from a strategic point of view one might suggest that Alexander the Great's attempt to incorporate Persia into the Macedonian empire was a failure.

Sources:

Engels, Donald W. Alexander the Great and the Logistics of the Macedonian Army. Los Angeles, University of California Press, 1978.

Goldsworthy, Adrian. The Roman Army at War: 100 BC- AD 200, Oxford University Press, Oxford, 1996

Lloyd, A.B. "Philip II and Alexander the Great: The Moulding of Macedon's Army” In A.B. Lloyd (ed.), Battle in Antiquity, 199-217. London, 1996.

Roth, Jonathon. The Logistics of the Roman Army at War (264 BC- AD 235), Boston: Brill, 1999.

PS: You find the Romans boring? The horror...