First things first; Prague has a lot of tourists! However its massive charm is more than enough to make this one of Europe's most impressive destinations.
Prague is one of the most beautiful cities in the world. I can not think of a setting I have seen that can beat the combination of Vltava Charles Bridge, Mala Strana and Prasky Hrad (Castle). The beer is the best in the world and competes to be the cheapest (and I would like to point out this is not just in terms of Western Europe this is still the cheapest quality beer I have come across!) This would be enough for me but Prague throws more at you. Staromestka namesti (Old Town Square) is taken directly from a fairy tale, Joefov is one of the oldest Jewish settlements in Europe, Vaclavsky Namesti (Wenceslas Square) is dripping with contemporary history. On top of this you have one of the densest clusters of Art Nouveau art anywhere in Europe; with Obcedni Dum ranking amongst the very elite of this style in architectural terms. Then there are the outlying parts such as Vysehrad to add to this. All is then mixed with an artistic heritage which even by Central European terms is amazing.
And it is only once you see all this you can appreciate why you will no longer have Prague to yourself. It may have changed a lot since 1989 but this is still a city that should feature highly on any traveller's itinerary.
The best advice I can give is just to go off and explore (the same with every touristy city). The main drag between Staromestka Namesti and the castle is very impressive however this is the focus of the crowds. Delving into side streets to find hidden gems like Valdstejnska zahrada (Wallenstein Garden) exploring the bars and clubs of Nove Mesto will help you see that there is more to Prague than shops selling communist nostalgia to Western drinking parties. Prague is an astonishing city and the small amount of effort required to lose the crowds is all that is needed to find a highlight of Europe.