Right, and increasing science cost per population favors wide empires who can build more Universities and Research Labs that give flat science boosts. It also involves a choice. Both are dumb mechanics though; if tall empires need a boost to science it should be done by giving tall empires a boost to science, not by arbitrarily nerfing wide empires.
It's not a choice if it's strictly better to have an empire with more cities to build science buildings in as opposed to tall cities with high population to make those fewer science buildings more powerful. The entire bonus that tall empires get from Tradition and Freedom is a massive food boost, because in order to catch up with wide empires on science, you have to get huge cities. Even with the science penalty, tall empires still have less effective science than wide empires (don't forget, even a tall empire has a small science penalty because they have more than one city). If you cause population to work against science, you instantly turn Tradition into the worst tree in the game, because you want your population to stay small. There's no choice involved in that.
The fact of the matter is, Wide empires needed the nerf; it wasn't arbitrary. When more pop = more science, and smaller cities grow faster than tall cities, and each different city grows simultaneously, wide empires simply have more science... and more production, more resources, more gold, more luxes, and so on. The only thing they arguably have less of is happiness, but with ideologies giving free happiness to already-necessary buildings, wide empires have never been stronger. The nerf needed to happen. You might argue that trade routes removed their gold advantage, but if you really think that, you haven't tried trading post spam with the full commerce tree on a wide empire. Once you do, you'll want to nerf commerce. You can have the largest army in the game on top of so much income that you don't even need trade routes anymore, you can set them all to internal and make your cities huge... and since it reduces the upkeep for roads, city connections are also more effective.
Wide was always strictly better, the problem is that going wide was not limited by effectiveness, but by the fact that the AI often settles the good land so quickly that you often don't have more than 4 viable city locations without going to war. It's "harder" to go wide because you can't just sit there and have it happen on high difficulty, the AI forces you to get your hands dirty. That's why when you do it right, you're rewarded handsomely... prior to BNW, too handsomely. Look at
this thread from before BNW, hell, before even GNK, offering ways to nerf wide empires. Notice how severe some of the OP's suggestions are, and notice how everyone loves the ideas, because it was seen as necessary. Notice how quickly the BNW science penalty gets suggested, except their proposition is even more severe: 5% per city...
per era. Be glad we didn't get
that one.
You're still rewarded very handsomely for going wide in BNW. The science penalty now correctly nerfs people plopping cities anywhere they want, but as long as you build your cities up with science buildings and food, which is easier than ever with internal trades (which Order is getting a buff to in the fall patch), your science is still better the wider you are. That's not an arbitrary nerf, that's how the game should work.