When you have so many converging hypotheses that lead to the same conclusion, it may be called a theory, it does not invalidate it ... In biology, for example, it has already been proven :
http://fr.wikipedia.org/wiki/Évolution_(biologie)
Indeed, as you point out there are convergences from where the use of genetic or other trees and this speech is extremely attractive (if only because any other opinion like the earth is round, the earth does not is not the center of the universe, etc. is considered to be heretical and sectarian).
This kind of convergence was found with HIV and shared by the large majority of the medical world, and heretics have been and are the subject of all the sarcasm of their opponents (genus Dede). So these are not arguments and counter arguments but a simple opposition in principle.
If this step is not taken, everything else is discussed in a vacuum.
There is little more than the phylogenetic tree where we find some hypotheses, but not so much because we doubt this globally, rather out of prudence. Again, if you are a detractor, bring proof that works or at least some protocol (s) that hold water!
Same thing: what protocols? Like AIDS, vaccines, nuclear, chemicals and more?
But in principle, all options are open, therefore. it is not contradictory to say that a wall is blue if it has the measurable Kelvin degrees corresponding to its color ...
I am a technician by training and professional and I know the possibilities and limits of devices designed and manufactured for a well-defined use and not beyond. So a measure is neutral, it does not take sides for or against the use that will be made of it ... humans yes!
So concerning the theory of evolution, it (its interpreters) retains only what goes in this direction and considers that all the grains of sand of the machine are not to be taken into account. However, it is the grains of sand that stop the machines and scientific research also serves to highlight these grains of sand in question. The (somewhat old) example of the coelacanth is ONE of these grains in question.
Same thing you have to change the thread!