well Mede is dead....
However, The Elder Council has to recognize someone as Emperor before they can technically take the throne, do they not?
I don't see them Acknowledging her claim to the Throne... because she was dead, and the only way to no for sure it was her (and not someone masquerading), or that she was not under the Control of a Necromancer would be to light the Dragonfires, which Post Oblivion Crisis is pretty much Impossible.
but, to those saying "no, Septim Dynasty is done, its the Mede Dynasty now", the Mede Dynasty is no more either
Spoiler Mede was killed by the Dark Brotherhood. you have to remember, in TES All Events are canon, its only the person who does them that is not. as such both the DB Killing the Emperor and the DB being defeated are canon (The "them being defeated" is just when the Sanctuary is raided and they move to Dawnstar).
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As such, I am sure the Elder Council will be searching in some form or another for some Relative of the Mede Dynasty. but if they can't find one, and a sudden descendant of the Septim Dynasty appears, I can see them possibly acknowledging their right to rule (Similar things have happened IRL with various European Monarchies).
However, I see them more likely the Elder Council would assign a Potentate before they would ever acknowledge Potema as Emperess