Okay, so I've been doing some more thinking and I believe the best way to improve upon this game is to "simply" remake it, not in Python, but rather in Godot.
I've been waiting for literal months to hear back from a group where I can get taught Godot and GDScript, while also trying to get a hold of a friend who's already familiar with the engine in the meantime, but so far I'm getting nowhere.
My idea is to start out by aiming to replicate the gameplay of the most recent version 1:1, if possible using the assets from the original as to circumvent the need for additional art being produced, and then once that's done to continue adding and refining stuff from that point onwards.
Main focus initially would be to just make a version of Slave Matrix that can reliably run smoothly in HD.
Obviously this project needs to be open-source and available for anyone to work on, I really don't think I could pull this off on my own. I still only have surface-level theoretical knowledge about all of this, and that's nowhere near enough to make an enjoyable game.
If anyone who's already competent with Godot and GDScript wants to start this off now instead of waiting for my autistic ass to get around to it then that'd probably be the best possible scenario IMHO.
Tl;Dr:
Godot
1:1 Replica
Optimization
Improvement