LOVE this idea, can't wait to try this later when i get home.
Perhaps as suggestion, option (on by default) to completely remove the vanilla system, so basically the modules :-)

Nice idea, I added an option (off by default) to hide the vanilla quality modules (items, crafting recipes, upgrade recipes).
You still have to do the quality module research as a prerequisite for this mod's research.

Sweet Thanks!!

I tried enabling the option, but the vanilla quality modules are still there.

Do you mean existing modules in machines or inventories (which will stay even when hidden) or the option to craft them (which should be hidden/inaccessible)?

In the technology tree

I left those in to not mess with the technology tree. The epic quality unlock depends on the first quality module, and I used them as prerequisite for my own technologies.

Perhaps for immersion purposes it could be made so that also the technology icons itself no longer look like modules?

That should be possible. Do you have any suggestions for replacement icons?

Perhaps just the any quality icon?
https://wiki.factorio.com/images/Any_quality.png

With perhaps an "I" on top of it for the module 1, "II" for module 2 and "III" for module 3?

-- OR --

Quality module 1 actually unlocks the standardizer + Post processing building, and then you can use the icon of that post processing building plus the "uncommon" icon.
Quality Module 2 unlocks the Calibration building and you can use the icon of that building plus the "rare" icon.
Quality Module 3 unlocks the reinforcement building, and epic quality. so you can use those respective icons.

Only the last one is a bit annoying because Epic is a separate research after quality module 3 that also is a prerequisite for the legendary research.
Not sure what to do there...