We are planning an April three wk trip starting in Madrid, then Toledo, Seville, Granada, Cordoba. That brings us to our last six nights, flying out of Barcelona on the seventh day. Should we rush up to Barcelona for the last six nights, or is it worth it to stop in Murcia or Valencia on our way there? We would be relying on train or bus.
You could head in the direction of Barcelona but stop for a night and some daytime hours in Zaragoza, which is right on the rail line between Madrid and Barcelona. Zaragoza is a very interesting city, and it's considerably less touristy than your other destinations.
I can’t speak to the trains aspect, but Murcia is a nice small city good for a full day. Its Alcazaba is worth visiting and the city has a nice market. It doesn’t compare to the boquería in Barcelona, but nice nonetheless. I’m not a huge Valencia fan, but its sights can be seen in a day too.
Acraven’s suggestion of Zaragoza is a good one. One could easily spend 2-3 days visiting it.
Córdoba to Murcia will be a long bus ride, for a city that I only find moderately interesting. Valencia is easier (you can go by train via Madrid), but Zaragoza is a better choice logistically speaking, and does not need a lot of time to enjoy.