sonofjones said:

I get why he hasn't been a threat as a trained Jedi, but he should've been seen as a threat as a rebel. He was the one who destroyed the Death Star and the Emperor and Vader know this.

Up until recently with the new Dark Horse Star Wars title it was always held that they didn't know who it was. At least not for a while. In between SW and ESB, Marvel comics made it an ongoing mission of Vader's to find out who was responsible for the destruction of the Death Star and they'd show him hunting down rebels and questioning them until he found out.

So it wasn't supposed to be until shortly before ESB that they finally found out who he was.