I have been following this site for a couple of years, but recently started reviewing comments and trying to participate in more active way.
A couple of years ago, my wife and I traveled to Prague and stayed at the Prague Marriott Hotel. The location of this hotel was great. It was a 5 minute walk to Old Town and the Charles Bridge and the hotel did upgrade us and gave us access to the Executive Lounge. There is great public transportation which we did not use as walking to any of the sites we wanted was very doable. We stayed there 5 nights and then we traveled down to Vienna.
We arrived in Vienna and we had a reservation (also 5 nights) at the Imperial Riding School Renaissance Vienna Hotel. This hotel upgraded us as well with access to the Club Lounge. The location of this hotel was not quite as central as Prague, but it was quite convenient to getting to the downtown area. If you go by foot, it will take about a 1/2 hour. We took the commuter rail, station was 2 minutes away, and switched to the Metro. All and all, it was about a 15 minute ride to downtown. Right outside the hotel there is a trolley (tram) line which (we did not take), but it does go to the downtown area.
We had a great time in both cities and I would be glad to share the sites and activities that we did in each city.