13 nights in Spain Itinerary help

If you're don't go to Granada then I don't understand why you'd fly into Malaga. If this will be your only trip to Spain, ever, then I understand your itinerary, if not, then I'd break the country down by region and base your itinerary on that. I'd hate for you to spend the majority of your vacation traveling between places. You are correct about Granada, other than the Alhambra there isn't much else to see. In town there is the Mirador de San Nicloas that affords a beautiful view of the Alhambra and also the Royal chapel where the tomb of Ferdinand & Isabella is (no photography allowed inside the chapel). The cathedral is nice, but does not compare to the one in Sevilla. Depending on what time you get into Toledo, one night may not be enough.

2 nights gives you one full day. Even if you land in the morning, it will take hours to get through the airport, to Granada and settled in your hotel and you'll probably be pretty zonked after - at best - only a few hours sleep on the plane. By then you'll probably want to find a place for lunch. Take a nap. There's a Moroccan market next to the cathedral. Walk around the Albaicin, working your way up to the Mirador de San Nicolas for the best view of the Alhambra at sunset (around 7.30). Then maybe a light dinner and a good night's sleep. The Alhambra will take most of Sunday. It is very large with long walks between the major buildings. And it's your first full day - don't underestimate how much jetlag can drain you.

Going from Seville to Toledo means going all the way to Madrid and doubling back. Since you only have time for one night in Toledo (which will mean at best about two half-days), I'd consider just spending all those nights in Madrid so you don't have the hassle of the extra hotel change. If you can get an early start, you can see a lot of Toledo during a day trip. I spent three nights in Toledo and loved being there in the less-touristy evening, but for just one night... And with luggage most folks will want to take a taxi to and from the Toledo train (or bus) station, though there are escalators so it is possible to walk.

Why fly from NYC to Malaga if Malaga does not figure in your plans. Start in BCN and finish in MAD.

-Arrive Barcelona - 4 nights
-Fly to Granada - 2 nights (check Vueling)
-Train to Seville - 3 nights
-Train to Toledo - 1 night
-Train to Madrid - 3 nights (day trip to Segovia)

I like it! If you feel Granada is too far out of the way just stay the first two nights somewhere on the Costa del Sol.