Take Astrophysics for example: we know how neutron stars or white dwarfs form but of course they also could have been created by some omnipotent being. Or can you rule that possibility out?
A rock that you find somewhere in the mountains could have been formed deep in the earth's crust millions of years ago but there is also the possibility that it was created by an omnipotent being and placed just where you found it only a day ago. It's possible after all.
So according to your logic every branch of science has to leave the door open for an intelligent designer but somehow this is only an issue with the Theory of Evolution.
Therefore an intelligent designer isn't an explanation at all. You only know that he did it but not how. If this designer is a supernatural entity then you'll never figure out how he did it because the supernatural is per definition not understandable by natural minds (if it were understandable then it wouldn't be supernatural). So once a supernatural designer is accepted there is no need to look for further explanations.
An intelligent designer could have created all species that ever existed but if he did then he did it in a manner that they look as if they evolved. So why assume his existence? Only because we think it might be cooler if we were designed as if it were if we only evolved? But why do many people think it would be cooler to be designed (even if the design is sloppy i.e. as if we evolved) instead of having evolved?
Evolution doesn't offer the best solution only a solution that is at least better than the previous one. Many systems in our bodies are indeed very complex but suboptimal. We are not able (at least at the moment) to build such complex systems but nonetheless we are able to see that their principle is flawed. Take the human eye as an example: it is a very complex organ and it surpasses every camera we can build but the nerves and blood vessels are in front of the retina. No one would build a camera in that way. Sure we can but that wouldn't be very intelligent. However, this is absolutely fine with evolution because evolution works with the material it has at hand so we don't have to expect perfect design because there is no intelligence behind. (It's compareable to a bush that has to grow through a maze. The walls of this maze are made of lasers for example so they cut off a branch if it tries to penetrate the wall. So only those branches continue to grow which don't touch the walls.)
Yet this camera works better than any camera we can make! The bat's sonar is also better than any we can make also. To call these organs "wrongly made" when we do not even understand them and cannot make anything better is totally wrong. When you do not know the reasons, when you cannot do better, you cannot criticize the work of another.