What nerf would make rationalism not the "best pick"

Per title. Rationalism is always the best choice and is often what prevents the player from falling behind on the higher difficulties. In multiplayer I assume if the game gets that far it's the pick too because you end up always having better equipment than the other players.

Something like halve the opening 5% bonus and reduce the bonus to universities, etc?

Personally, Free Thought's +1 science from trading posts is probably the strongest single benefit from the branch, if leveraged properly. That being said, I think it's the fact that it boosts science in so many different ways that really makes it such a strong choice. Especially considering science boosts are practically non-existent outside of Scholasticism (in the Patronage tree). Your mid-late policy branch choice basically boils down to Aesthetics for culture victory or Rationalism for almost any other circumstance.

The +10% from the opener isn't really that strong so dropping it to 5% wouldn't hurt the tree as a whole much; however, I could see a case for possibly switching this bonus with the +1 for science buildings from Sovereignty. Secularism's +2 from specialists is relatively weak. The Great Scientist boost feels right, plus it tapers off in effectiveness quickly as Great People are born. The yield from the boost to RAs can be amazing or terrible depending on the situation.

Free Thought seems to be the sore thumb as far as I'm concerned. The trading post bonus alone can be used to increase science output by a dramatic amount not to mention the secondary +% bonus (that is roughly equivalent to the opener's bonus depending on how many Observatories you have; assuming you have a University in every city that is). The only question is do you just nerf the policy into the ground, or perhaps move it to require every thing else in the tree to be taken first, (or a little bit of both)?

Fist of all, I have to say that in order to have Rationalism not default as the best choice, you need to make the social policy trees that it competes with not-crap. That means major overhaul of Commerce, Exploration and Aesthetics imo. When that's said, I'd move the flat science bonus when happy from opener to finisher, and I'd cut the science bonus on specialists from Secularism from 2 to 1.