I also would want to see how Kages would fare against Madara had Onoki been in his prime. Dude was the only reason they survived against Madara that long, I imagine that a Onoki without back pains and old age would prove to be quite a challenge and they actually, with Onoki as the only fire power lol, could fight against Perfect Susanoo (which was, several times, shown to be perfectly beatable by Bijuu/Bijuu+ level characters)
Kishimoto apparently wanted her to fight Tendou on top of the Hokage building and for her to be the first one landing a punch on Pain's main body, but his editor denied the idea as anticlimatic and wanted Naruto to be the first.
Revenge and all, Pain pissed at Tsunade's front door way harder than Naruto's, him devastating Konoha and telling Tsunade it was justice, this would've been a perfect stand for her as Hokage and also a nice way to show her prime skills (since she was rusted from not fighting for long in part 1). Tsunade punching in Tendou's face would've been quite the satisfaction.
Other than that, any prime Orochimaru fight. Also would've loved Kishi drawing a fictional Itachi vs. Pain.