I have stayed at both. They are very different experiences, so it depends on what you want.
Pension Suzanne is located in a non-descript building about a block away from the Staatsoper. Once inside the doors of the hotel itself (as opposed to the doors of the building), it offers an old-world Vienna experience with rooms decorated in a more antique kind of fashion. The owners are awesome -- super friendly and happy to provide guidance on what to do/see and where to eat. Breakfast is lovely -- good choices and served in a nice breakfast room (and breakfast is served on china, as I recall).
Motel One is a simple but sleek hotel chain. The Staatsoper hotel is in a cool old building. The interior is decorated with trendy furniture in the nifty brown and teal Motel One color scheme. The front desk is professionally staffed and helpful in a corporate hotel kind of way. Rooms are small but functional. Room for luggage is fine for my carry-on size bag but limited if traveling with a lot of bags. Breakfast is a decent spread, but there is an additional charge for it.
I would give the nod to Pension Suzanne for what feels like a more Viennese experience.