I'll grant you that explanations in evolution often read like "just so stories".
But it might help to understand that the theory of evolution makes several different claims.
The first claim is that the Earth is old, many millions of years old. The evidence for this was already persuasive by 1800. The second claim is that all creatures on Earth descended from a common ancestor. This idea predates Darwin, indeed his own grandfather Erasmus published these ideas. The evidence for this by now is extremely strong: the relationships between species visible in their anatomy are now observed to be mirrored in their genes (where related species even share harmless mutations or "spelling errors" in the genome). It must be emphasized that these two ideas have essentially no opposition in biology.
But the third claim of evolution is the mechanism for the formation of new species: natural selection, where chance and necessity sculpt life. This is where there is debate, and exactly where you point out. The controversial theory of punctuated equilibrium was introduced to why evolution appears to happen in relatively rapid spurts separated by long periods of little change.
The weakest points in evolution is agreed to be the lack of credible explanations for the origin of life itself (3.8 billions years ago, the date of the oldest fossil-bearing rocks). It certainly wouldn't surprise me if there was "intelligent design" involved. But I am confortable with the idea that God used evolution to sculpt life; life capable of evolutionary change would be resiliant and adaptable, and I can imagine God taking pleasure in the unexpected and beautiful outcomes of evolution. This is as the Catholic Church and the mainline Protestant Churches teach (I am Episcopalian). (It also wouldn't surprise me if intelligent design, God's active intervention in evolution, was also behind the very rapid rise of modern humans.)
By the way, life does not violate the law of entropy (the second law of thermodynamics). This law states that closed systems cannot tend towards greater complexity. But the Earth is not a closed system: it receives a huge amount of energy input from the Sun. And, to the point, most life is powered by the Sun (through photosynthesis by plants). (Except for those ridge vent worms, which live off the bacterial communities that feed on the chemicals and heat from the vents.)