More than 10 years later, BJ still gets a lot of credit for his initial UFC run, which was very impressive. He gets a pass for his second run at WW because he was always undersized and somewhat made up for it by putting together a half decent title run at LW. Once he started to decline, the narrative simply became "He's getting older, prime motivated BJ would have won those fights" (and maybe he would have).
People forget about the fact that the entire community pretty much had Frank completely written off after the accident. He broke his femur and took a long time to recover. When he came back, he looked fat, sloppy and not at all like his former self. So there was a period of about 2 years where everyone thought Frank was done. Then he racks up some impressive wins again, it looks like he's back, but for all his impressive wins post accident, he has an equal number of losses. And nobody said after any of those losses that "prime" Mir pre-accident would have won those fights, because the fact is that he wouldn't have, he became a better fighter after the accident (if you had told anybody in 2004 that Mir would actually develop pretty decent stand-up, they would have laughed at you).
The two stories, or rather the way we tell the stories of their careers is just different. BJ will forever maintain an almost mythical status of "Motivated BJ Penn at the right weight class can beat anyone". Mir on the other hand is the HW that came back from a severe injury and managed to get back to the top 10, but not really the top 3.
Personally, I believe Mir deserves just as much credit as BJ. We discount the fact that BJ didn't do fuck all at WW after his first win over Hughes too easily. Sure, some of those fights were extremely competitive (e.g. 1st GSP fight) but the fact remains he lost those fights. Then when you look at his second run at LW, he was dominant, but the fact is there were better LWs at that time. I would have loved to see him in Bushido and later Dream rather than fighting Stevenson or Sherk. But as I said in the first paragraph, no matter what happens, people will always think of his first run in the UFC when they think of BJ and use that to paint a better picture of his whole career than perhaps it deserves.