What criminal cases were there where the evidence initially seemed to strongly point to one/many innocent person(s) as the perpetrator(s), only for a different look at the evidence to lead to the real perp(s)?

Not sure this is an answer to your question, but I hope it's a useful contribution.

The people responsible for planting the bomb that brought down Pan Am flight 103 over Scotland were known early on, but never brought to justice. Instead two functionaries (who were involved, but nor directly responsible) were charged, and one was finally punished.

Pretty much everyone involved with the investigation knows this. It was easier to go for the low-hanging fruit rather than deal with the real villains.

Jim Swire, whose daughter died in the attack has a website: http://www.lockerbietruth.com/

Take a look at the bits that deal with the Lockerbie bombing.