On the molecular, cellular, and physiological levels there is no substantial difference between humans and non-human primates. On the molecular and cellular level is no substantial difference between a human and a frog. On the molecular difference the difference between a human and a fungi is minimal.
Well then I'm glad to see you at least don't deny all science.
This suggests, amongst other things, that if there is indeed a creator, he (or she, or whatever) was not very creative at all. If humans are so special then why are we made of a collection of recycled parts - shouldn't we have dramatically different parts?
Not very creative at all? Because the universe somehow wasn't enough?
Look at it this way. If you were an inventor, and had free run of any kind of materials, processes, manufacturing, etc that you wanted, would all your creations look the same? How much does the space shuttle look like a bicycle? Yet the physiological carry-over from a coelocanth to a human is enormous. It wreaks of lack of creativity, at the very least.
The Creator plays by the rules that are there
I thought the creator sets the rules. Again, if you have free reign to do everything - as implied by the adjective almighty - why just make little tweaks? Why not try things that are radically different?
And if humans are so special then why have we been on this planet for such a short period of time? Reptiles had the run of the place much much longer than mammals have. What was the point of a long age of reptiles if the goal was to produce humans?
Above my paygrade. I don't have the exact dates, nor do I grasp how your making this long/short call.
Modern humans have been around for at most 2-3 million years, depending on how generously you define "modern" and "human". The Jurassic era itself was around 60 million years, and encompasses only a fraction of the total amount of time in which the largest and most dominant vertebrates were reptilian.
Now granted there is a chance that humans could survive another 60+ million years on this planet without extermination (at their own hands or otherwise), but that still leaves the question of why a creator would bother to leave the dinosaurs at the top for so long if his ultimate creation was still yet to come?
And for that matter why produce humans which such a flawed physiological design?
My best answer is that reality is what it is, with intent to produce maximal liberty.
I'm not familiar with this new sense of liberty that you are applying here. A great number of physiologists, science fiction writers, comedians, comic book creators, and young children with crayons have proposed better ways to design a human body - which do not in any detectable way impede on liberty. What about the current design contributes in some way to liberty?