I would always pick the alternative that goes with subs. There are many good reasons, but one of the main one's is the ability to put an EQ in line with the subs. That plus a high pass filter will almost always give you the chance to get better overall bass response in a room than trying to get the same from just two large main speakers.
Then there's a litany of other benefits, like increased dynamic range, lower main amp stress... etc.
I recommend the use of the AM Acoustics room mode simulator to help you place your speakers and listening location, careful measurements and GIK soffit traps in the corners if needed. If you do all this well you are going to have a very difficult time finding a system that performs better in bass speed, impact or system dynamic range and clarity.
