Before you laugh, remember, he struggled with Doug Jones and Henry Cooper in 63. Prime RJJ was an upgrade to both and a similar size.
I don't think Jones will do too well against any heavy that he doesn't have a distinct speed edge over. He may still be faster than Ali but not by much. On the other hand I don't think RJJ's power translates that well to heavyweight. I can't see Ali being too troubled by Jones in that department.
Personally, I think prime RJJ was as good as Jones and Cooper. As for size, D. Jones was a light heavyweight turned heavyweight and Cooper would be a light heavyweight if he fought in the 90s. In fact, he'd likely have been a RJJ title defense at light heavy. Same with Doug. So I don't think RJJ would be too small. I favor Ali, but in 63, he was still developing and wasn't just plodding over light heavyweight sized fighters.