The pops themselves aren't that much more complicated. About the biggest differences I can see is that each pop is an actual person who may be an alien or a slave or a rebel. That and there's an in-built method to move pops between colonies (I think you still can in Civ it's just non-obvious and kind of janky)
Aside from that, they're a food-based number that grows and harvests/works on a specific tile. Same as in Civ.
In Civ, pops are literally just a number that grows based on food and harvests/works on a specific tile. That's it. Pops from one civ are identical to pops from another civ. There are no traits. They don't have happiness. They don't rebel individually. You can't purge/enslave pops in Civ (not that you'd want to, because they're all the same). Soldiers aren't recruited from pops, because "pops", as an abstract game concept, simply do not exist in Civ.
You can argue that the pops in Stellaris "aren't that much more complicated" but you're wrong. Pops in Stellaris have many interlocking systems developed around them, while pops in Civ have
nothing. Pops in Stellaris genetically modify themselves to suit their environment better. They have an ideology, they join factions, their happiness is tracked, they migrate by themselves to worlds with more similar ethoses, they can be purged or enslaved, they have traits. It's not as deep as Victoria 2, but calling it not much more complicated than Civ 5 is the most ridiculous hyperbole I've heard today and really downplays the entire system.
Consider this: in Civ 5, pops aren't even tracked by the game because, for all intents and purposes, they don't exist. Population is kept track of per city. It is an integer that goes up or down, depending on growth or starvation. Every single "pop" for each city in Civ can be tracked with a single integer. They are fundamentally, intrinsically linked to cities. They're more like a city's "level" than anything resembling a population of people. A city could have 2 pops or 20 pops and all that changes is one number.
In Stellaris, pops are a core game mechanic that can be modded and extended. They possess a species, traits, faction, ideology, and happiness. This means somewhere in memory, the computer's storing
at least these five variables per pop. In terms of complexity, this is vastly beyond Civ's "one variable per city". Consider that Stellaris can have 1000+ star systems. Assuming a conservative 0.5 habitable worlds per system, and 10 pops per world, Stellaris would track 5000 individual pops. This isn't even taking into account the additional game logic to allow for pop behavior/decision-making, which is obviously executed per pop.
I understand people are annoyed that Stellaris pops aren't tracked Vicky 2-style, but there's a huge continuum between Victoria 2 and Civilization. Stellaris is much, much closer to the Victoria 2 side than the Civilization side.