It's an interesting question! On one hand, the Seleucids put a lot of stock in remaking Syria into a sort of counterpart for Macedonia - establishing through their naming and ideology counterparts for the cities of their distant homeland. But part of this is perhaps a symptom of being cut off from that homeland - of having come to terms with the existence of a Macedonian state independent from theirs ruling the homeland - and thus finding that they had to recreate their origins in a different space.
Since the Ptolemies were never in a position to take Macedonia, it's hard to say what they'd do. But for Seleucus, his return was, i believe, always described in contemporary writings as a sort of spiritual and physical homecoming, the return of the old King at the end of his life. Thus we have to acknowledge that Macedonia would always have immense spiritual and political importance.
But what is a pcaital in the ancient era? Every major city and settler colony had a Royal palace of some nature in the Seleucid era, so that it could serve as the capital. Administration from Pella would be nonsensical. The major treasuries, harbors, military fortifications, etc. would remain where they were. The bureaucrats would remain in the major cities of the East, or follow the King on campaign or tour. The Seleucids might be a bit more focused on the West, perhaps appointing a member of their family to govern there as they traditionally gave their sons the Upper Satrapies to govern.
The biggest impact I think would be intangible - a sense of ideological or societal unity that the Seleucids had to put more effort into constructing OTL, and different narratives. Perhaps more Seleucid Kings would return to die in Macedonia at the end of their lives, aping Seleucus. Macedonia and control over it would have an immense spiritual and ideological impact on the realm, and would facilitate the distribution of settlers across the East and probably shore up Seleucid authority in Thrace and Northern Asia Minor more, while creating liabilities with regard to Epirus and maintaining control over all the Greek cities. A genuine policy of autonomy might behoove them there, a light hand in the style of Antigonus Monophthalmus.