Component A: One of the issues with the Stellaris tech system is that you can't directly deep dive to get to a specific end game tech. If I want to do a megastructure build I can't deliberately research all the way up to megastructures while ignoring side-chains, I have to come at it sideways using various weighting systems that still rely on random chance.
With a more traditional tree it's much easier to get the sweet zone where a slow researching empire can still get the specific end-game content they want while a fast-researching empire just gets more end-game techs and a bit faster. Since launch Stellaris had needed
every empire to get
every tech to make sure they get the techs they actually want or need. This is a big part of why empires start feeling pretty samey, because one of the standard 4x playthrough differentiators just can't be used for that.
Over the past bit though they've been adding in more ways to get keystone techs, especially with the new focuses and the much more frequent techs from core events. If you're able to get all the techs you want or need as a low research empire without researching all the techs then you no longer need every empire to be able to research all the techs so it makes sense to slow down the tech to get the playthrough differentiation I mentioned earlier.
Component B: In the buildings and districts model an early tech planet was limited to 11 research buildings of 2 scientists each and those science buildings were competing with amenity buildings, civic buildings, and so on. With the new pop growth model it's harder to get new pops to fill new jobs but with the new district/zone/building system it's much easier to make some of those jobs be new scientists - even your starting homeworld has 2.4 scientists compared to the 3.14 starting 2, and just upgrading your city district 2 or 3 times will get you as many scientists as a whole second building would have before. So scientist output needs to go down to compensate or everyone will be working off the old broken void dweller science economy.
E: Component C: And as
@Abdulijubjub said, there's a bunch of previously additive multipliers that are now fully multiplicative.
Combining all these you're looking at a pretty hefty drop in base per-scientist output. They probably went too hard with a full drop to 4 from 9(12) and a lower pop per district count, especially with all the booster buildings locked behind t2+ tech, but I'd say that's the basic reasons.