Well, there's the monthly tick, and then the rest...
Free up a system from a monster by 2420 and watch your computer crawl as all empires rain on it like plague on the poors.
You could have less planets in your galaxy.
I usually play 1K stars, max empires, 125% planets. Slow down begins by 2300 to a 2400ish tedium.
I tried 1K stars, 10 empires, 25 % planets. Ten 6-7 planets blobs with the occasional green dot in between. Desert. I got only a 20 years offset of the slow down.
So it seems severely tied to number of bodies on the map. The AI has to consider them, regardless of number of empires.
The first of the month is when PDX decided to update the entire game state for all empires.
The game has to update empires the same day to maintain coherent relations, etc... It would be good to spread the load over the month but result would have to be stored in a buffer and applied on month tick. So more RAM taken for less CPU strain.
This is quite the reverse philosophy of what used to be done when hardware was not so RAM friendly. I suspect old engine code to be at work here (nothing to do with x64), and depending on how deep are burried in it concepts like unit, path, ressource collection and the likes, it could be quite tricky to fix without breaking anything.
But I trust the Stellaris team in that they can't give us all that juicy end game content and abandon us in front of a lag wall.

And anyway let's see the improvements to displaying ships tomorrow. That is already a big hinderance.
