The point of the empire pop penalty balance seems to be you have three choices come the mid-game: Conquest, Co-operation or Stagnation. You need to find external sources of pops or resources, rather than sitting in your corner and breeding pops. You can't just ignore the rest of the galaxy and expect to thrive.
I honestly like it. It makes Raiding for pops a viable strategy for xenophobes again, and adds new factors into the Tall-vs-Wide discussion rather than 'Always Wide because Bureaucrats remove the downsides of wide'. It also makes it easier for empires to recover from a territory loss by giving them a population boom to bring you back up to speed. Makes the power structure of the galaxy more dynamic and come-from-behind victories possible.
And you can take advantage of that and basically be the Reapers/Wraiths, cyclically raiding for pops, letting an empire rebuild, then starting a fresh harvest.
A significant change it strategy you need to do in 3.0 to maximize pop growth is build your city districts before you need them. A planets free capacity increases the population growth rate. No more sitting carefully trying to time the building with the pop appearing optimally: Build a planets infrastructure straight away. Even then, your non-core worlds population should probably aim to be around 40.
If you wanted to sweaty it, you could always make vassals, let them rapidly breed, then integrate them to take advantage of their rapid growth. Less sweaty is it makes a feudal-type empire more viable, creating vassals from your sectors rather than owning them yourself.
In short, I think the change is overall a good one but it does require you to completely relearn how to play with the new pop system. Old strategies simply will not work, and I think that there is a bit of people:
a) Trying the old ways of growth and being annoyed they don't work.
b) Being off-put by the AI doing a better job of keeping up with the player, making people feel like they're doing relatively worse than they actually are.
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So, bets on the next DLC? I'm betting something to do with Primitive Civilizations. They're due a rework, and the current Enlightenment/Infiltration was already a proto-Archeology system so I can see it being updated to use that instead.