The bigger rear tire helps with the 2up business. I don't know about the last years model but in 2007 the FXSTC had a larger rear tire than the Dyna had. I have a softail but I personally like the standard V twin over the B motor.
I compared the same two bikes in 2007 along with the deuce and bought the wide glide. The wg fit better and handeled a little better. If I were making the choice today I would probably go with the custom.