My half-baked idea: Make beakers come mainly from specialists. Make specialists cost money. Make money come mainly from trade and resource acquisition. Make bettering your trade and resource acquisition something science is not very good at.
As far as what science would do, it should let you do new things, but not necessarily improve the things you're already doing. For example, pursuing science would open up the orbital layer, which is a new thing you can do. Or science could let you terraform, when normally you couldn't. Obviously, doing new things will improve your performance, but it will only do so through your smart decisions rather than a mostly automatic bonus.
The incremental improvements to your efficiency that you get through science right now could come another way: make successive specialists of the same variety in the same city cost less money. That way, you get better at production or trade or culture by managing your population. This would also help combat ICS. (Is that still a thing?)
Anyway, that's my half-baked idea.
As far as what science would do, it should let you do new things, but not necessarily improve the things you're already doing. For example, pursuing science would open up the orbital layer, which is a new thing you can do. Or science could let you terraform, when normally you couldn't. Obviously, doing new things will improve your performance, but it will only do so through your smart decisions rather than a mostly automatic bonus.
The incremental improvements to your efficiency that you get through science right now could come another way: make successive specialists of the same variety in the same city cost less money. That way, you get better at production or trade or culture by managing your population. This would also help combat ICS. (Is that still a thing?)
Anyway, that's my half-baked idea.