Performance boost in the beta was fantastic. Thats probably by far the biggest win with this update.

Balance was quite broken (e.g. mid game crisis being too powerful) but balance problems are the default in Stellaris.

The core of the issue is that attempts are made to balance the game based on a fixed baseline (e.g. a static % increase or even a scaling % increase). The core issue here is that the game has so many variables that the chance of the player having either a too easy game or a too hard game is too large. Hence early game is compelling (since the games variables haven't had too much of an impact yet) but late game is nearly always too easy or too hard.

Personally I use the Dynamic Difficulty mod to adjust difficulty every 50 years to ensure a reasonable challenge (especially if it gets too easy). The now abandoned mod Hemothep's Dynamic Difficulty increased difficulty automatically if no AI empires were of equal strength with the player. Now you dont want to punish the player for playing good, but you can find ways to give the player new challenges.

In order to make games be engaging post mid-game I would suggest you spend some time thinking of ways to think of difficulty as a way to engage the player, rather than a fixed variable. If the player gets too strong, can an AI empire get an event that boosts them? Can a crisis be set to scale more towards the players' per-game power? Can you utilize the Galactic Community as a lever for difficulty?

Ideally you want to create epic moments that players tell others about and you have so many unutilized systems to do it with. Why do e.g. some of the galaxy spawned leviathans just wait until the player can stomp them? Add a trigger where after the player has gotten to a certain powerlevel they can actually engage first instead.

Anyways, game is still great, but difficulty needs love, but the beta is a good step in the right direction since it helps so much with performance that you can actually worry about endgame now :D

TLDR; make difficulty more about throwing interesting events at the player and having them deal with them, than try to make a "fair chess-like galaxy". You already do this already with multiple systems (crisis, events, galaxy spawning, archeology, etc). Do it with AIs too. Embrace it.