I feel that conditioning is a weak rune because WR relies on snowballing so much.
Giving up on immediate buffs like adaptive carapace, bone plating, or loyalty for 5 minutes of nothing makes your early game that much weaker.
This isn't a big deal in the mid lane or jungle, but it seems important for baron and dragon lane since it's a game of attrition.
I've had so many fights where I've won with a sliver of health, and, had I taken conditioning instead, I would have lost.
And because of how short the games are, you don't stack up that much armor/MR, making the end payoff not that rewarding.
And as mentioned, it's better for squishies since armor/MR has diminishing returns, but squishies can't afford to not have bone plating or adaptive carapace in the first 5 minutes.
I use conditioning only for ARAM or for bruisers like Galio.