Hi *******
The preservation of soft tissues is an unexpected bonus, exactly the opposite of a "problem". Similarly, the survival of archaic lifeforms is not a problem. Were ichthyosaurs to be discovered in Loch Ness, or pterosaurs in Pakistan, that would be a wonderful new field for study. Sadly this does not often happen.

As for "flexibility", that is better described as toughness. When evidence comes forward that contradicts the current understanding, it is studied, and if found to be true, the theory changes. That's science. Like wrought iron, it bends to a new shape, but doesn't break. (As an aside, it's really difficult to beat swords into ploughshares. Carbon steel is hard and springy, not tough and malleable).

If you really want to find out about the wonderful world of the (sometimes successful) prediction of the forms of transitional fossils, read some of the excellent popularising writers- Stephen Jay Gould is very good. You'll also read about failures, because failures are sometimes as important in science as successes.