I am flying into Frankfurt next summer and am wondering if this is too much to try to squeeze in for 16 days including travel? I dont want to stay in Frankfurt too much but I do want to goto Paris for 5 days, Berlin for 5 days and maybe Prague for 3-4 days. Does that sound like enough time? and what is a good way to do the travel?
Well, the city center of Frankfurt is worth an afternoon and a dinner (Frankfurt has got a great local cider restaurant scene and nightlife). Download that free guide book. It describes a great historic walk thru the old town of Frankfurt: http://www.frankfurt.de/sixcms/detail.php?id=317578&_ffmpar[_id_inhalt]=177743 Then actually you should spend at least one, better two days in the middle Rhine river valley, which is only around 60 to 90 minutes from Frankfurt. Then from Cologne take the Thalys train to Paris. From Paris book a low cost flight (airberlin.com, easyjet.com) to Berlin. From Berlin take train to Prague but make sure you interrupt the journey for a few hours in Dresden. From Prague take train back to Frankfurt. If you don't want to do the UNESCO world heritage protected middle Rhein river valley there's also a high speed train connection from Frankfurt to Paris (3.40hrs for downtown to downtown service).
Bryan you can make this work if you fly out of the city of your final destination. If you have to get back to Frankfurt to fly out then I'd skip either Paris or Prague.
The best advice I can give to you is to plan on staying in one basic region for that amount of time. You can see a lot of different things between Frankfurt and Paris or Frankfurt and Berlin. If I were making this trip, I'd plan on spending time in no more than 2 large cities and then finding other things to do in the meantime. For example, around Frankfurt you can either spend time on the Rhein/Mosel and work your way towards Paris. Or you could spend some time in central Germany and the northern edge of Bavaria on your way to Berlin.
One thing to remember, in this amount of time, don't backtrack unless it's completely unavoidable. If you have to make a loop then that's fine. But keep going somewhere new as you go. That way you will maximize the amount of things available to you.