The Stellaris game setup menu is already a cluttered mess, I have 2000 hours and I have no understanding of how half the options affect the meta, idk how anyone else manages
No offense intended, but that is very much on you. Apart from reshuffling the options in another order (not sure it needs to), there's really not much that could be made clearer there. Unless by "meta", you mean knowing that the AI has an additional -10% reduction on ship upkeep from Captain to Commodore, which... Is really not something I need to know precisely, at all.
Each supported ruleset increases the number of interactions the devs have to balance exponentially.
Not for everything, though. While I strongly disagree with the proponents of "no balance at all" (like in the case of MEs being OP), no, Stellaris isn't a perfectly balanced game and shouldn't be. Especially since the whole purpose of allowing more options at game start is to unbalance things up (see my example of "no rare resource manufacturing", the whole point is to shake things up hard).
Something as prosaic as "Hiveminds on/off" would require a radical overhaul of the local enemy seeding for Pacifist empires because Hives and Machines are the one neighbor they are actually allowed to expand into.
... Which they already need to do for the people who don't own the relevant DLCs (reminder that you need Utopia to have Hive Minds, and Synthetic Dawn for Machine Empires). And it's also a bad example in that "spawning near a HM/ME" is too situational to be relevant to the actual balance of the ethics. Pacifists aren't designed with the idea of military expansion in mind, them being able to invade gestalts is just a fringe case with no major, reliable impact on their efficiency.
The main one: Related to 2; I don't want Stellaris to be a game where I need a PhD in game design myself to be able to calibrate the galaxy setup in order to produce a satisfying emergent narrative. That's what I pay Paradox for. Every time there's a menu option for the player, that constitutes and abdication of responsibility for the devs to make the game, y'know, right the first time. "Oh, you didn't enjoy that playthrough? It's your fault because you didn't calibrate the galaxy settings correctly :^)" is a cop-out and I don't want to pour more fuel on its fire. I'm the player, not the dev; these settings should have been tested and optimised and hardcoded in 2016, not left as some sort of esoteric cryptic puzzle for me to have to complete through a hundred hours of iterative testing before I'm allowed to have fun.
If you dislike player choice so much, you might want to avoid a game whose first thing you do as a new player is having to chose how to design your own empire. Unless giving that choice to the players (a choice that is relatively more complicated and impactful than "do I want my galaxy to be ovoid or do I want it to have four arms?") is also a cop-out and an abdication of responsability from the devs ? I'm sorry, but I just don't understand that argument, at all. Stellaris' entire appeal is player choice. Most of the development of the game since 1.0 has been focused on giving the player more choices, in the form of more authorities, more mechanics (traditions, civics, etc.), more events... And yes, sometimes it's a bit chaotic, and with a certain kind of learning curve. But it's also sort of the point ? It's not really a game of competitiveness, for that you might want to look for other games that are more tailored to this use.