Sannin are better vs Madara because...
J-man and Orochimaru are both experts at sealing techs, Orochimaru also knows alot about Edo Tensei, as he completed it, then Kabuto boosted it further
J-man and Orochimaru both know about the Rinnegan, J-man because he trained Nagato, Oro because he figured it out through research
Oro pretty much immortal, I mean he smashed the shit out of 4-tail Kyuubi and didn't get burned like everything else, only other person to do this was Nagato, if Madara even has Amatsuru it wouldn't effect Oro nor J-man, Oro for shed skin jutsu and Jman for sealing
Even with Mokoton, Orochimaru knows all about that, hes the reason Yamato has wood release..
Plus they know each other like Naruto/Sasuke/Sakura, so there teamwork is superior as they all know what each of them can do, plus EXPERIENCE, they went thru the 3rd shinobi war togather and lived..all 3 of them are kage level or above..
Orochimaru was going to be the next Hokage if he hadn't went evil, the 3rd stated that himself
J-man was second choice after 3rd died, but refused
Tsuande is current Hokage..
so yeah..
Oro is used to breaking Genjutsu, and J-man has quite possible the strongest genjutsu seen so far
ontop of all this you have Tsunade who is expert at healing if either of them need it, plus her super strength can break through Madara's Susanoo, as seen recently..giving J-man/Oro an opening to do some major damage/seal
Its just the fact that all the other kages are experts in one type of skill set, Onooki dust release, Raikage Lightning, Mizukage Lava/water, Kazekage sand/earth/some sealing
When comparing these to 3 Sannin who of which 2 have a huge aresenal of jutsu, J-man and Oro, plus the best medical ninja with super strength, Tsunade..its just a better match even tho there is only 3 of them