Tsunade tops Jiraya as hokage. They both would have been destroyed by pain in confrontation, however Tsunade saved lives in the process and Jiraya couldn't.
Though if he was hokage, with Tsunade helping him the pain invasion would have gone well too, seeing as he could fight and she remote healed. Also Naruto would have never been pushed to learn SM which would leave Jiraya with imperfect SM and no intel vs pain.
As for Paperwork and stuff, Tsunade does that better too. Also if he was hokage Tsunade might have ended up having to go on the mission he did and would have died, or escaped who knows.
Jiraya couldn't test Madz much more than her either.
As far as i see it the original sannin barring maybe orochimaru arent as far apart in power as people might want. Things would have gone pretty much the same.
Also who thinks Jiraya and kakashi combo could defeat pain. Don't be silly, kakashi was made short work off especially with his stamina and reserves which are worse than Tsunade during pain arc. Jiraya would have lost him as a teammate very quickly. And Gai wasnt around.