I think you'll have time for a day-trip to Toledo while you're in Madrid. Especially if you're not big art-museum fans. Toledo is on a spur railroad line connected only to Madrid, so you can't just stop there on the way to another city (as you can with Cordoba).
As far as I'm concerned, for non-art lovers Madrid is visually less interesting than Cordoba and Toledo. For that matter, if you end up deciding one day of sightseeing in Madrid is enough, you could also day-trip to Segovia. Cuenca (medieval hill town) is great, too, but I think it's unlikely you be able to get a reasonably-priced, spur-of-the-moment AVE ticket to and from Cuenca, and that's the only way to get there fast enough to make Cuenca a viable day-trip.
There's a lot to see and experience in Seville; three nights is short there. You may still be suffering from a bit of jetlag on your first full day in Seville.
Edited to add: I enjoyed both Malaga and Valencia but they were part of a much longer trip to Spain. I'd rate them behind Cordoba and Toledo for sure, and both require considerably more travel time from the places you have locked in.