If you are easily awed by ruins, a history buff like me, then just add this to your itinerary in Kota Gede. It won't take too much of your time to see this mosque.
The entrance of the mosque was like an entrance to a candi or Hindu temple. Imagine what it had witnessed over hundreds of years. The walls in the mosque's courtyard still has carvings of hinduism, which makes it unique.
Do read up on it before visiting as there aren't much info on it. Go to yogyes.com to find out more.