Couldn't agree more and was exactly what I was gonna say. She didn't lose to Pain and honestly we don't fully know her capabilities. We know she is extremely strong and her main goal from the beginning was to help the villagers. Remember Shikimaru's comment? Pain went from guerrilla warfare to an all-out attack (almighty push - shinra tensei). Am I saying she could have beat Pain/Nagato, No but she wasn't beaten.
This woman is from what we know the best medical shinobi in history. If you ask me I don't think it is a Kekkei Genkai because honestly, what Kekkei Genkai can you think of that is honestly going to stop Madara? It is definitely something she knows about Madara whether she learned it from her grandfather/granduncle/being the Hokage
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"There's no mistaking it...It has to be Madara's Jutsu!...Tsunade-Sama at this rate..."
This is coming from Shikaku, a very, very intelligent Shinobi. Tsunade has got to know something to counter/void out Madara's Jutsu.
Tsunade does not get a lot of credit because we look at the other Hokage and Kage-level ninjas and they have these awesome abilities, but Tsunade is a true Senju and by that I mean she is pretty much good at everything. Extreme Raw Strength/Taijutsu, Intelligence, HUGE chakra reserves and on top of that she is able to use her medical skills for Offense and Defense. Think of her Offensive Medical Skills as an analogy to the Byakugan Gentle Fist skills: She can cut off Chakra pathways and what is a shinobi without Chakra? Oh yeah and she can regenerate cells at an incredibly fast level and even replace organs if I am not mistaken (With her Creation Rebirth Technique), which kind of makes her immortal in a way. (I know it shortens her life every time she uses it but if she has to use it in a battle, good luck to the opponent).