I'm getting the notion that most of you think Sage Mode is a weapon itself when it's just really something that enhances the abilities you already have.
If Jiraiya > Naruto without Sage Mode, then Jiraiya > Naruto with Sage Mode.
Think of it this way:
Jiraiya = 9/10
Naruto = 7/10
In terms of power, without Sage Mode. Now let's say Sage Mode allows you to have twice as much power...
Jiraiya = 18/10
Naruto = 14/10
By this thinking, Jiraiya was still stronger than Naruto. However, Jiraiya wasn't able to enter Sage Mode by himself, and even then it wasn't perfect. I'd say this is the only aspect that Naruto surpasses Jiraiya in.
In the end though, it all comes down to plot. Naruto could have beaten Pain w/o the Kyuubi's help but if the Kyuubi never went on rampage in the Pain arc, Naruto would have never met Minato. And if Naruto had never met Minato, then the plot would have not proceeded the way Kishi wanted it to...