Well in a way, the idea I mention go back to the days that Piety and Rationalism were incompatible - but I do think when we are talking about Rationalism and being overpowered-through-universalism it's worth to drag religion into this discussion, because I feel the game is not completely balanced in that regard - the original intend according to the developers was to have religion play a major part in early/mid-game but lose importance from renaissance/industrial era and onwards. However, I don't really think they accomplished that. Having founded a religion will be a major factor in the success of your empire, not only in early game, but also late game happiness and economy will be heavily dependant on your religion.
For those reasons, I do think it's interesting to consider the options of having some game mechanics that will make religion lose importance in late game, or alternatively forcing you to make the choice between religion or science. Obviously, the part here is getting the balance right. We all know that in GnK it was really a no-choice, because the bonuses offered by Piety (coupled with the lack of drawbacks of taking Rationalism) meant that it was all-but-never worth it to choose Piety. But BnW has gone a good way in making Piety more viable as a choice, and if the significance of religion waned over the duration of the game, one could step up Piety even further without skewing the balance completely. If at the same time choosing Rationalism meant foregoing some of your religious benefits, things might start to look a lot less clear-cut than now, where Rationalism is all but your default choice on the higher difficulty levels.
I don't really think religion should fall off drastically, given that the entire SP tree around it would get kind of pointless.
Most Pantheon beliefs have far more impact early-game than they do later on, and the Founder beliefs are only good if you put effort into it and win the secondary religion spreading game.
So I think religion is in a good place balance-wise, with its big rewards requiring investment and some work to accomplish.
Getting a religion also tends to set an Empire back some early, especially for the first few to found, and an edge early can snowball into a lead later.
Also, some civs are completely built around religion, so nerfing it to buff Piety would really harm them.
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Anyway, Rationalism, if it remains, needs to be balanced against Commerce and Exploration, which it competes with for selection.
It may be sub-optimal, but I've always favored Commerce over Rationalism: perhaps I see

as inevitable and

and

as the greater path to make the empire great.
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I admit to using a mod that buffs Commerce with these changes.
Commerce Opener gold bonus moved from Capital to the city with East India.
Entrepreneurship now gives +1 Gold to all Specialists.
Mercenary Army now gives Double Gold from Plunder promotion to all Melee/Gun units.
Big Ben now provides additional trade route slot.
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As well as the Game Balance [BNW] mod that lowers Secularism's

boost to 1

from 2.