Clap went through some major redesigns with the 4.0 release just three years ago. That wouldn't have been possible if clap 2.0 or 3.0 had been added to the stdlib. It's almost a poster child for things where libraries where being outside the stdlib allows interface improvements (date/time handling would be the other obvious example).

Rand has the issue of platform support for securely seeding a secure rng, and having just an unsecure rng might cause people to use it when they really shouldn't. And serde is near-universal but has some very vocal opponents because it's such a heavy library. I have however often wished that num_traits would be in the stdlib, it really feels like something that belongs in there.