Today, although I am staying at the MO from where I am making this entry, I went over and looked at a few rooms at the Charles. Depending on rates, I'd say it's definitely worth considering. I looked at a deluxe room at about 40 sqmt (one class above the minimum room) and an executive suite somewhere in the range of 60-80 sq mt.
Of course I could not judge service levels but the rooms were quite decent and appeared to be well-designed.
Location: the Charles is a few minutes walk from the Hauptbahnhof, the MO about 7 minutes walk from Marienplatz. If you are using the train, the Charles is very convenient but the neighborhood is definitely not as interesting and diverse as the Marienplatz area. From the airport, there is not much time difference to either.
Style: the MO is more "old world," the Charles more modern. The Charles has only been open 2 1/2 years.
Consortia: Both are Virtuoso but I believe only the MO is FHR.
Internet: Both charge an arm and a leg. The MO is E25 a day, the Charles E20.
For me it would be tempting to try the Charles next time. The executive suite I saw looked worth paying extra for, quite nice.
Also I did have the lunch included with Virtuoso (which the desk clerk said might be changing to a dinner, that would be cool) here at the MO and it was very good -- the hotel restaurant has a Michelin star.