Actually, we do have many instances in which the appearance of the phenotype can be predicted from the genotype. And research is turning up more details all the time. It is a logical fallacy to assume that because we do not yet have the knowledge of exactly how *every* gene contributes to phenotype, that we have *no* knowledge in that area.
What you’ve done is no more than suggesting a possible general mechanism—responding to chemical signals—which is only described on a microscopic level yet seems to be missing a lot of the details. I don’t think you can bridge the gap to show how shape is determined on a macro level.
Every multicellular organism has its shape determined by molecular events. There are no exceptions. The propagation of chemical signals throughout the developing embryo is hardly a "possible general mechanism"--it is the only mechanism. Those signals direct cells when to grow, when to stop growing, when and how to differentiate, when to die (cell death is an integral part of development), etc.
As far as not being able to "bridge the gap", the fact that it is not yet possible to look at a genome and predict the person's appearance is meaningless. That does not mean that it will never be possible. The fact is that many features *are* predictable from genotype. For instance, since a few Neanderthal genomes have been sequenced, it is possible to determine their hair color without having any sample hair.
As for transitional species—can you give me at least one example?
Only one? Humans.
Don't fall into the trap of thinking that there is a defined end point for evolution, and that either species are heading for that end point or are already there. There is no end point since evolution is a continuous process. Therefore, by definition, every living species is a transition species.
I didn’t say appearance, or features—I said shape. How genotype predicts shape on the macro level seems to be information that is entirely unavailable.
As for species transition—if evolution is true, then some species currently existing would necessarily be defined as precursors of other species also currently in existence. And by the laws of probability, some of the precursors would have to be very close to their successors in the evolutionary trajectory, while others would be not so close.
But we don’t have this. We only have some species which can be claimed to be on the same line of evolution as others, but only distantly related—and even this often seems a stretch of logic. There are none which are close together on the evolutionary timeline, as would have to be the case if evolution were true.