Sorry, it took me some time, but here's your answer (I did the best I could as a non-assyrologist):

This question has two parts that need to be answered: Why did Seleucus found Seleucia in the first place and why did he transplant some of the population from Babylon to Seleucia:

Let’s go Homer-style, hysteron proteron:

The reason, why Seleucus transferred some of the population of Babylon to his newly-founded Seleucia might seem fairly easy at first: Because he needed somebody to inhabit his new city and Babylon was the most flourishing city nearby. But this is AskHistorians, so lets dig a little deeper: When repopulating a new city there are some options: you could completely depopulate near cities, like Antigonus Monophthalmos famously did with Alexandria Troas, either transferring one city to another spot or, as Antigonus did, make one citiy out of several others. In Hellenistic times this could serve the purpose of building a better defensive system for a city or transfer the city to a certain spot crucial for your defensive system. Or you could just transfer some of the population to your new city and by that way ensuring that your city had the population that could fulfill your needs while leaving the other city more or less intact. Additionally especially Alexander and in his succession especially the Seleucids (though that practice also is reported for the Ptolemies) used to found military settlements, where they settled veterans of their respective armies with the aims of having a steady flow of new soldiers from that spot. Hellenistic armies relied heavily on people trained in the arts of the Macedonian phalanx, and those people were usually Greek.

As despotic as it may seem from today's perspective to resettle a large proportion of a city to somewhere new it might not have been: You had the opportunity to claim new ground, get onto a new market and often settle into a new infrastructure. Unfortunately we don’t know much about how those transferals were received in the population, as the literary sources don’t tell us anything about the thoughts of the common folk, especially if they’re not Greek. Pausanias, who records the transferal of the Babylonian (Paus. I 16, 3) goes to some length to show, how well disposed Seleucus was to the Babylonians, as he gave them their walls back and constructed a temple of Bel.

But as far as Babylon is concerned, the city continued to flourish under the Seleucids so not too much damage was done (as contrary to former beliefs of Seleucus draining the trade potential of Babylon on purpose).

But why did Seleucus found Seleucia in the first place? The date of the foundation seems to lie somewhere around 300 BC. There are some reasons to found a city in the Hellenistic times, who usually intertwine and overlap for every settlement: The first thing was of course to make your name immortal. That was surely the case when kings decided just to rename the city, as has happened to Nikaia, modern Iznik: Lysimachus named renamed the former city Elikore after his first wife Nikaia, of course by at least reshaping the city to some degree. On the other hand aforementioned Alexandria Troas was initially named Antigonas, but renamed into a neutral name by Lysimachos, who had killed Antigonos in battle and wanted his name to vanish from the earth. Secondly it was a way to represent your Greekness in your newly acclaimed territory: The people had to know who were the new masters of the country, and how to them better than planting an enormous temple of Zeus right into the heart of their country? But usually those were not “spots of Greekness in the wilderness” but Greek and non-Greek elements are blended together, as they are in Seleucia. Here archaeology seems to debunk the age-old myth, that Greeks and non-Greeks did not mix. The Hellenistic kings relied at least to some extend to the integration of the indigenous people. Another reason to found a (Greek) colony somewhere far from Greece might have been to supply your local governors, who often were Greek in origin, with a Greek infrastructure, so that they could still enjoy the Greek way of life, while administering say Mesopotamia. This was particularly important for Seleucia, who while (as we now think) not being the one “capital” of the Seleucid empire (like the Achaemenids the Seleucids used more than one administrative center to rule their country), was still an important center where much of the higher ranks of the (Greek) administrative apparatus Seleucus was to be stationed. In Babylon they would have to resort to a more Mesopotamian way of life.

Especially for the Seleucid empire there were two main reasons to found a colony: Military or trade. Especially the borders in the far east and in Asia Minor had to be protected from constant incursion of the Scythes (Bactria) or rival Greek kings (Asia minor). Here Seleucus and his successors established a extensive network of military colonies that he used to recruit his mercenaries from while at the same time having them present where immediate response was crucial for protecting what you claim to be yours. On the other hand he tried to protect the most important trade routes by lining them with new foundations. Here, Seleucia comes into play: It lay perfect to oversee the trade along the Tigris. This led many scholars to believe that Seleucus wanted to found an adversary for Babylon that would deprive it from its status as most outpost in the trade from east to West (From India and the likes through the Gulf of Persia and the Euphrates to Babylon from where the traders went by land to the coast of the Levant or Asia minor only to ship from there into the Mediterranean). This tale is similar to the founding of Alexandria by Alexander as a rival for Tyros when it comes to the Mediterranean trade. But as I said, the continuing importance of Babylon suggest that if this was the intention of Seleucus he was proven wrong by time. Also, what reason had Seleucus to hate Babylon? After all the accepted him with waving hands when he returned there in 312? A survey of the historic geography of the two streams by Adams has shed some light on this issue: Naturally, while the Euphrat had a gently flowing but unsteady stream, that would fall short in late summer and autumn, the Tigris had a much steadier flow, but on the expense of being barely fit for ships because of his dangerous streams. On the other hand it was a better source for irrigation, especially since the royal canal between them ensured a steady flow of the Tigris. This seems the reason why the Achaemenids constructed a net of weirs, that was used to make the water useful for irrigation not hinder enemies from entering the Tigris, as Arrian states (Arr. VII 7, 7 with Briant, p. 720). Still, the destruction of the weirs by Alexander improved the Tigris for shipping. Also, It seems that in the second half of the first century BC the imporance of the Tigris as agricultural region and a vein of trade had grown steadily (Adams, p. 192). Additionally the volume of trade increased: The Hellenistic Kingdoms went after ever increasing luxury and the fact that the whole trade route from the Gulf of Persia to the Mediterranean was in Greek hands facilitated trade. Tthe only thing that was missing was a big city that could serve as trade centre between east and west. Seleucus catered to that need by founding Seleucia. Still one should keep in mind that a Hellenistic emperor could go to great lengths to make his own name immortal. There is usually more than one factor when it comes to founding cities and the eagerness of the Hellenistic rulers would have been reason enough to found a city anywhere, but the potential of the location of Seleucia made this one easy for Seleucus.

Sources:

For the Seleucid colonies:

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• Getzel M. Cohen, The seleucid colonies: studies in founding, administration and organization. Wiesbaden 1978

• Paul J. Kosmin: Land of the elephant kings: space territory and ideology in the Seleucid empire, Cambridge (MA) 2014

• Susan Sherwin-White & Amélie Kuhrt: From Samarkhand to Sardis: a new approach to the seleucid empire, London 1993

For Mesopotamia:

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• Rober McC. Adams: Heartland of the cities. Surveys of Ancient settlement and Land Use on the Central Floodplain of the Euphrates, Chicago 1981 (cited as Adams)

• Pierre Briant: From Cyrus to Alexander. A history of the Persian empire. Transl. By Peter T. Daniels, Eisenbrauns 2002 (cited as Briant)

• Tom Boiy: Late Achaemenid ans Hellenistic Babylon, Leuven 2004