Is evolution completely scientific?

We can find puzzling questions in the evolutions which are under intense research and scientists are still to conform. Assumed evolutionary sequence states that fish gave rise to amphibian. This change would require millions of years and have involved many transitional forms. But no such series of fossils have been found till date.
There are puzzles in the phylogeny of animals. The first puzzle is that 60-80 different structural types of animals in the early Cambrian suddenly appeared. The second puzzle is that why no major new types originated in the 500 millions years since the Cambrian.
The principle source of new genetic variation is mutation. Most errors are due to errors in the replication process during meiosis that is not corrected by any mechanism. There is no mutation pressure. Most of the variation of genotypes available for selection in a population is the result of recombination, not of new mutation.
Is the evolution slow continuous change in gene of the organism? But we do have certain genetic fact that takes us to dark. The example of pleiotropic gene is one of them. There are pleiotropic genes that control most of the genes. So, what happens if changes occur to that gene? Will a new organism evolves with a new genetic makeup? If yes, why these are not described by fossils.
Mammals and Dinosaurs are a classic example of independent replacement but the molecular evidence questions the whole record. The fossil record shows the rapid rise in the early tertiary, after the end cretaceous mass extinction. But according to molecular theory the mammal and dinosaurs co-existed for about 30 millions years of cretaceous. This does not prove that mammals competed with dinosaurs.
Antievolutionists claim that there are limit to the amount of change that can be made. There is creationist like Gish who claims that there are some limitations within “basic kinds”, without being able to express exactly that why changes are restricted within them. Others claim that the limit lies in the availability of genetic variety. When limit is reached it ceases variation, “might conceivably be renewed by mutation, but whether this happens is not known,” of course it is unknown.