You seem to be under the impression that Roman legions were some sort of state-raised force. Until the Principate, when the emperor retained sole control of all legal recruitment, this was not the case. Although armies were voted on by the senate, these votes held no real legal weight, since the senate could not pass laws or order magistrates. Recruitment was carried out by magistrates holding imperium, and these magistrates held total control over their military forces. During most of the Republic military imperium was limited to the consuls (and, if necessary, the praetors). But consular armies had a limit on their size, which could not legally exceed four legions, although two consular armies could combine if both consuls were needed to fight a war. Proconsular armies, and provincial armies in general, had no such limit, so that even without an extraordinary magistracy (like Pompey's mandate to suppress Mithridates) a general could still raise an unbelievably large force. Legions were not bound in the Republic by any sort of "master list" in terms of their numbering. There were several dozen legions fighting on both sides at Pharsalus, and we need not presume that they were all numbered consecutively. More telling is the fact that after Actium, when Octavian found himself in sole control of over sixty legions, there were multiple versions of each legion on each side. Both Octavian and Antony primarily made their forces from a core of Caesarian troops, and so on both sides the old Caesarian legions were reconstructed (although we have some examples of legions, like the Ninth, that fully chose one side or the other) completely and given the same numbers. It was like that in the Republic generally, in that a general was in no way bound to number his legions consecutively with respect to already-existing legions--though we have no evidence for the numbers of the Republican legions at Philippi I find it very hard to believe that Brutus and Cassius respected the Caesarians enough to skip the numbers of Caesar's legions, and undoubtedly there were Tenth Legions on both sides. The "standardized" number and numbering of the legions is entirely a result of Augustus, who vastly downsized the army (remember, he had over sixty legions after Actium) and imposed enormous limits on the holding of military power and military recruitment so that nobody could challenge him. Even then, however, we find irregularities in the legion numbers all the time. You find duplicate legions pretty much constantly. These duplicate legions could form when a new legion was needed and so elements of two previously existing legions were combined (with the new legion taking the name of one of the old ones and the nickname "Gemina"). The "Gemina" nickname appears to have also been common when a legion was formed entirely from a part of a single pre-existing legion that refused to give up its traditions and numbering. And during times of civil war, such as in 64, A.D., we find duplicate legions everywhere, as rival generals raised armies and numbered them on their own systems. And there are also perfectly normal and easily-explained duplicates. Since a consular army was composed of four legions, the First through Fourth legions were the most common legions in the Roman army. They had duplicates pretty much all the time, though, because often a consular army was raised if reinforcements were needed and would be by default composed of the First through Fourth legions--but of course since they already existed they were duplicates, receiving usually a special nickname (although duplicates weren't always given different names, which makes identifying them really difficult).

So basically, yes the Republican army was vastly larger, at least by the 1st Century, B.C., than that of the Principate. However, there was no "core" of legions, as you put it, since magistrates holding imperium raised and disbanded their troops as they pleased.