Never been to Prague before, but we decided to visit Petrin hill as a first step.
Just do this. We crawled up the Petrin tower and it offers you a view which will make you fall in love with Prague.
You can take the funicular train up to the tower, but you don;t need to be in great physical shape to get up the hill. So if you don;t drag along too much stuff, climb it by foot. You will enjoy the parks and the nature, you will see along the way and it does not take too long. Might even be faster than queuing for the train.
There is plenty of stuff to see. Must see is the Petrin tower. If you have small kids I guess the mirror maze or the pony ride is nice. However you can also wander of further off in the parks. Bring a pick nick and enjoy the peace and quiet.