I think maybe QuestGAV has hit the nail on the head.
There's a number of things going on here, (1) the crowd that saw both of them pitch (of which I am one), and the crowd that saw only Pedro pitch. In addition, few of us would argue that Koufax was a well respected "person" in baseball, while Pedro leaves a lot to be desired. Looking at the stats, Pedro edges out Koufax in many categories - and comes woefully short in the ones Koufax dominated in.
The reality is that from a "talent" standpoint, these two pitchers are AWFUL close. From a personality standpoint, Koufax wins hands down.
From the group that never saw Koufax pitch, all you have is the stats and Pedro, again, has the edge. From the "old-timers" standpoint, we saw them both - and most (if not all of us) think Koufax was better.
Both sides can find quotes from all kinds of individuals that say one was better than the other - simply confirming the judgement is split.
Unless we could put both of them on the field at their peak, we'll never know for sure, but the bottom line for me, anyway, is that if they were both free agents today, and each wanted the same money, I would choose Koufax. If he would have stayed healthy, I think he would have proven he was better. He was 30 years old and had just put together the best 4 seasons of anyone of his time or before. Had he pitched an entire career, I don't think we'd be having this discussion.
In my mind, THAT is what makes him better.
One final thing that might explain better where us "old gys" are coming from - or at least the way I'm looking at it...
The 4 years from age 27 to 30 were probably the best of both pitchers (to date for Pedro). If you average those 4 years for both players, you get the following. It's hard not to imagine how good Koufax would have been had he pitched another 6-7 years. Pedro's numbers suggest a heavy reliance on the bullpen.
Maybe the way Koufax pitched is what ruined his arm - maybe he would have fell flat on his face the next year even if he was healthy - but these are the last 4 years us oldtimers remember. He was the absolute best of our time - and has a mystique about him very similar to Ruth in some ways. It's fun to wonder what he might have done - and yet to be determined what Pedro will do.
http://www.bigcitybaseball.com/library/pandm.jpg