I feel like for sure they've said that empire size is going to be some function of districts AND systems, but I can't find it, maybe it was on the steam or something, but I don't have time to watch. I might just be totally misremembering though. They could make systems worth holding into with the changes and tweeking numbers, but if I'm not wrong about empire size including systems the fundamentals are still in place to make systems not worth it.
Pretty much ninja'd by Telgin. It might remain small compared to districts, but planets are getting bigger (in some ways, smaller in others) as well, so the relative benefit of systems (and thus the decision on if they are even worth having) is going to go down as well.
It's pretty clear that the devs are trying to address snowballing through at least three mechanics here (influence, tech penalties and pirates), but you could probably make an argument that snowballing is half of the point of playing a game like Stellaris.
Ultimately I'm fine with anti snowball mechanics so long as they do well and the game is still fun. The issue with the tech penalties from systems is it ultimately fails to achieve it's goal as an antisnowball mechanic, you still want to snowball as hard as possible and have as many planets as possible. It just makes it so you don't want to own the space in between the planets as you snowball though the galaxy.
Similarly I dislike the pirate mechanic because it both really doesn't matter that much and is only an annoyance and not a fun mechanic, and also it's main purpose seems to be a weak patch job on the failed mechanic of system tech penalties. To punish people for playing in the way the game works instead of actually trying to change the systems so that it's not massively less efficient to play the way the devs want you to.