I like to think that it's not so much that it's a transitional phase, it's just that the "updated version" is capable of surviving on its own.

Example (with Simpsons influence):

A fish spontaneously mutates a third eye and the brain capacity to take advantage of it. This allows it to see better than other fish with two eyes. It survives and mates, which produces more three-eyed fish. These three-eyed fish keep surviving and mating, etc. Two-eyed fish are still around and doing just fine for themselves, they just don't happen to have three eyes. The fact that the three-eyed fish succeeds does not necessarily mean that the two-eyed fish dies out. In some cases that does happen but not necessarily.

Same deal with apes and people. Just because we exist and are able to keep going doesn't mean that apes are no longer able to survive. At some point this might be true but for now they're doing fine for themselves.

I guess that kind of is a transition phase also. Slightly different, but yeah.