Alright, I think I might give this one a go.
Starting with the issue of transitory fossils and lack of living species of the same evolutionary branch.
Go out into your backyard or an open field or park, and think of how many animals have died there. Now think back, if you are a young earther or an old earther, to the beginning of life. How many animals would have died there from then until now? How many deer have you seen dead on the side of the road, or squirrels or birds? And how many skeletons do you see? Now dig down several feet and tell me how many you see.
My point is, most skeletons do not survive the natural breakdown of biological materials. It requires a special situation for a skeleton to be preserved for long periods of times. I am almost more surprised that we have as many fossils as we do from the prehuman species of australopithecus.
Now to address the issue of two subspecies of humans existing at the same time.
The most prominent theory for the origin of humans is the out-of-Africa theory. If all humans got their start in Africa, one would not expect to find much outside of Africa until the circumstances were right. A primate in Africa would be adapted to warmer weather, it would require the development of substantial brain power before a primate would be able to move north into colder climates due to the lack of ways to stay warm. This severely limited the range for prehuman primates. By the time a primate would be developed far enough to move out of the region, it would already be mostly human. This is why you don't see chimpanzees, gorillas, or bamboons outside of Africa except in zoos, they are not adapted for bordering climates.
Now consider the fact that human beings, once they began to spread out, would still be mostly in the same gene pool. Until humans crossed over into the Americas, there was ample opportunity for exchange between different human groups. This would have prevented much further change because the requirements for survival had already been fulfilled and all the groups were sharing the same genes.
Also, look up Homo floresiensis. I think you will be surprised to find out just how recently this species lived alongside human beings without ever being destroyed.
Feel free to critique this or raise questions, I am more than willing to answer questions.
