You (well, EY) make a good point, but I think neither the Pluto remark nor the fish one is actually an example of this.

In the case of Pluto, the transNeptunians and the other planets seem to belong in a category that the asteroids don't. They're big and round! Moreover, they presumably underwent a formation process that the asteroid belt failed too complete in the same way (or whatever the current theory of formation of the asteroid belt is; I think that it involves failure to form a "planet" due to tidal forces from Jupiter?). Of course there are border cases like Ceres, but I think there is a natural category (whatever that means!) that includes the rocky planets, gas giants and Kuiper Belt objects that does not include (most) asteroids and comets.

On the fish example, I claim that the definition of "fish" that includes the modern definition of fish union the cetaceans is a perfectly valid natural category, and that this is therefore an intensional definition. "Fish" are all things that live in the water, have finlike or flipperlike appendages and are vaguely hydrodynamic. The fact that such things do not all share a comment descent* is immaterial to the fact that they look the same and act the same at first glance. As human knowledge has increased, we have made a distinction between fish and things that look like fish but aren't, but we reasonably could have kept the original definition of fish and called the scientific concept something else, say "piscoids".

*well, actually they do, but you know approximately what I mean.