Seville, Cordoba or Malaga?

Most likely Sevilla. But it may depend on where you are coming from and where you are going after. Only two days for southern Spain? Then I'd say "none of the above."

Sevilla is a major city with lots of attractions that easily fill a few days. Plus it makes for a good base for some daytrips (though your won't have time).

One could easily spend a couple of days in Cordoba, and I always encourage people to do so instead of a quick stop or daytrip. But I'd pick Sevilla over Cordoba when given an either-or choice.

Sevilla is the best of the choices. It has more to see and 2 days is a pretty good time for Seville outside of the big festivals (when you would want more time). The Alcazar, Cathedral and surrounding quarter are outstanding. You can also stroll down to the river to see the Golden Tower. Depending on when you're there, they may have bullfights (if that's something that interests you). At night you can also see a flamenco performance - this is where flamenco originated.

Thanks for your thoughts!

I put high priority on museums and Malaga has two relatively new ones that are well curated,
but you'd be crazy to go to Malaga if you've never been to Sevilla and have Sevilla as an option!
I think Sevilla is worth a week!