The science enhancers huge +150% (and 1 module slot) can actually be matched by 7 legendary productivity modules (+25% per), or 5 modules and +50% base productivity. This means the cryoplant can outperform the enhancer, and the EM plant can match it, even in vanilla factorio. This problem is even worse if there are mods adding higher quality levels or higher tier modules.

A fun idea I had to fix this is adding more module slots with higher quality science machines. +1 per quality level (+2 on legendary) would result in 7 slots in a legendary enhancer, allowing you to easily keep up on productivity or even use other modules (that's a lot of quality :D ). I do not know of any other machines with this property, so it would make the enhancer even more unique and fun.

Actually had that idea, but deemed it unimplementable, cause quality does not support it, at least it seems so, will welcome any suggestions

I have seen mods such as https://mods.factorio.com/mod/more-quality-scaling use auto-generated machine variants to get otherwise unsupported quality effects, and "simply" swap machines on placement. It may be worth looking into...

A few other ideas I have are:
-Scaling the enhancers productivity with quality
-adding a repeatable tech that improves only the enhanced recipes
-multiplying the output of the autogenerated recipes (probably just the science output)
-Another "tier" of enhanced science using magic tesseracts (normal or rich?) with better output (more output multiplication, or another repeatable? Both?)

Yes, I quite enjoy this machine. How could you tell? :)

I would actually really enjoy your first idea (with the slots increasing with quality). Though I don't plan on implementing it, it's too much effort. I welcome anyone to submit PRs:)

I think I found out how to do the quality module slot thing:
https://lua-api.factorio.com/latest/prototypes/CraftingMachinePrototype.html#quality_affects_module_slots

I believe it was added in version 2.0.56
https://wiki.factorio.com/Version_history/2.0.0#2.0.56

I stumbled across this earlier today. If I am understanding it right, you should only need to set quality_affects_module_slots to true and it should work!

Thanks a lot, check it out now:)