I would like to point out, though, that just because there are a few things that we don't understand doesn't mean the whole theory of evolution falls apart.
It's not that evolution has holes. It's been well established on the small-scale. But the larger picture - the "protozoa-to-hominid" picture, which is what people think of (incorrectly) when you say the word "evolution" - doesn't have holes either. Holes are lack of information. What we have is information that
conflicts directly with that larger picture.
There are ideas out there attempting to explain this.
That is philosophy, not science. Science was very backward until people stopped putting the cart before the horse - the classical system of four elements, the concept of "humour," etc. are all examples of people coming up with ideas of how things work, then looking at the world to confirm their hypothesis. Science is done properly when the world is observed, then what we see is described. When you reverse that, you throw the door wide open to speculation and error. It is a natural tendency - it's easy to form opinions about how the world might work, but it takes a lot more work to go out there and look at it in-depth. Leave the pedants to their speculation; we need none of it.
We also don't know how the Egyptians built the pyramids. Are you also skeptical of the belief that they did it without help from magic or aliens?
Fallacy of false dilemma. I never said I thought species just magically appeared, that's your assumption. Say this were a court case, and we have a murder defendant. So much evidence points to the idea that he was in the room at the time of the murder, holding the weapon... but he has an airtight alibi. Do we say pixies killed his alleged victim? Do we say he was in two places at once? No, we begin looking for another possible explanation by looking for more evidence we may have overlooked.
I've read several hypotheses about the construction of the pyramids, and perhaps one of them is true, but perhaps none of them are true. That doesn't mean they did it with magic (although that
could be an explanation, if the physical "laws" were different then, and their methods would be impossible today), it just means we haven't come across the right explanation yet, and more investigation will be necessary.