First of all, no theory, including relativity, gravity, etc. have all possible evidence recorded for them. We have not measured the bending of every beam of light, the acceleration of every possible object under gravity. And yet no one has ever used that to discredit those theories as if they're not complete.
The important thing is that every fossil we've found to date fits into the theory of evolution.
Let's talk about the whale evolution again. The order of events is as follows:
- Someone noticed that whales and dolphins, despite seeming a lot like fish, shared some qualities with mammals, like blowholes and live birth. At this point someone made a prediction that dolphins and whales might share many more qualities, based on the idea that all species are related. An idea which comes from evolution. Without evolution there would be no reason to predict that whales have other characteristics in common with humans, and yet...
- Upon observing dolphin skulls, we find that there are TWO holes in the skull where the blowhole is, despite there being only one blowhole. No one would have any reason to predict this except with the idea that the species is related to other mammals. Certainly, there would be no reason to design them that way.
- Further, we observed that the dolphin skeleton contains bones which very much resemble legs and feet of other creatures, despite not having anything like that function. Again, no one would have reason to think these would be here, and yet evolution predicted it.
- Then we found really old skeletons of creatures that looked sort of like whales but different. They had way bigger leg and feet bones, and nostril holes in their skull way closer to the front as in most land mammals. Okay, that doesn't prove anything. But then someone predicted that we would find a skeleton with characteristics between that old whale-thing and modern whales. No one had yet seen such a creature, and yet somehow we knew it probably existed.
- Lo and behold, we then find a skeleton of an old creature - it doesn't matter how old, but it's older than whales and younger than the really old one - which has nostri holes between the front and the top. And the leg bones are smaller than the really old one's but larger and more defined than modern whales. WOW, what a huge coincidence, right? How lucky evolution got! Oh that's right, you don't believe in luck. So explain these observations and how evolution knew that they would be found before anyone else did. Seriously, explain it.
Then explain all the other thousands of similar predictions evolution has made over the past century and a half.