That's not a penalty though. You can't sacrifice ANY research to gain another type, you just gain extra society research. There isn't a negative to this other than people not liking it being an uneven number apparently.
So, prior to 2.2:
- You could sacrifice society research to gain more engineering (or physics) with the same resources.
After 2.2:
- You can't do that; if you want more engineering, you can't sacrifice your society to get it, you just need to spend more.
You're not just gaining extra society research. You are gaining extra society research
because you're not gaining
even more engineering research.
From an economics #s viewpoint, prior to 2.2:
- you could build a second mine/farm/power plant/lab to get +100% minerals/food/energy/research output
- you could upgrade a mine/farm/power plant 3 times to get +50% of the base output each time
- you could upgrade a lab 3 times to get +33% of the total base output each time, BUT +100% of the output of the specific research type you chose
After 2.2:
- you can upgrade any building to get +150% of the jobs, and therefore +150% of the output
So, before 2.2, upgrade gave you +150% minerals/food/energy, and only +100% science, but +300% science of the one you wanted and +0% of the other 2. After 2.2, they give you +150% of everything. So yes, you
are paying for that extra society output. That's basic economics. Nothing is free. You can look at it as "before, I was paying in society research to get engineering, and I can't anymore" or "now, I'm paying engineering research I used to get to get more society" but either way, you're saying the same thing.
Now, that's not to say it's a bad change. It does make selecting your science focus impossible, and therefore removed that choice, contributing to blandness, but there may be a very good balance reason for it. Or maybe there's not, and they just didn't want to program a 3-way upgrade path and 3 new types of jobs. But saying it's just free research is ignoring how the game works (and used to work) and how economy works.