I think some people may be missing the reasoning behind why population control is being made more unwieldy.
Currently Stellaris has a lot of mechanics... that players never have to deal with because they can reliably turn them into non-issues and forget those aspects of the game exist. Suppressing factions for example, selectively purging faction/ethically divergent pops, selectively enslaving faction/unhappy pops, tossing all unhappy planet-factions into one sector to reduce the number of factions to suppress.
That's too simple, too abusable.
So to address that, factions are being changed so that you HAVE to interact with them and then deal with the consequences of your interactions, no more one-click problem solvers.
Species-wide slavery and purging is designed so that you can't just cherry-pick dissidents, but actually have to either pacify everyone or fight ethics divergence the old fashioned way. Unrest on planets is being introduced so that revolts WILL (like they logically should) happen under oppressive regimes and the oppressed, impoverished, unhappy pops WILL be less efficient.
If you don't want planets to be unproductive messes constantly on the verge of revolt, don't fill them to the brim with billions of people who despise you. Resettlement will probably be the best way to counteract unrest buildup, but in the end, if you are playing a warmongering empire of slavers and sapient cuisine connoisseurs... you kinda have to live with the consequences of it ^^ Just like all-welcoming egalitarian xenophiles will have to deal with factions, divergence, limited expansion avenues and the sheer expenses of trying to keep everyone happy.
Strategy games are at their most boring when they start to play themselves. Perfectly functioning empires, lack of internal and external threats, complete domination over everything in the galaxy are all lovely power fantasies, but... if it's as effortless as it's now, then the entire charm of the fantasy evaporates.