GEM had puppets produce zero science
Not quite, it had them produce zero science per pop, right?
So for an X pop city, in GEM they would give 0 science with no buildings, they'd give X/2 with a library, 2X/3 with a university, etc. and any other science boosts would apply normally.
But now they give 1 science per pop, but with a -75% modifier. So a pop X city gives X/4 with no buildings, but gives 3X/8 with a library, etc.
So they're not quite the same.
And in GEM there was no per-city science penalty, and in GEM puppets had less unhappiness per pop.
Also, what seems like a bug is that occupied cities function like normal cities except for +1 unhappiness
I think this might be a GEM bug that has been carried over. I think they're supposed to give an extra ~0.25 unhappiness per pop, and production penalties?
Anyway, definitely these issues need to be cleared up.