Bacterial pathogens may use polysacchride based capsules to avoid exposure of PAMPs and antigens within the plasma membrane. In this way they can go undetected by the immune system [1]. According to Dr. Tapping, even if a B cell receptor recognizes the capsular polysacchride there will be very little proliferation and minimal immature IgM antibody secretion. No Helper T cell activation will occur because thier receptor must bind polypeptide antigen. This is where conjugate vaccines come in; which are small samples of polysacchride conjugated to peptide toxoid. When polysaccride and internalize the whole molecule. Then, the peptide antigen portion is displayed on the B cell membrane using MHC-II. Helper T cells can recognize this peptide antigen and binding of B7 to CD28 leads to costimulation, isotype switching and antibody maturation. All of the mentioned leads to the immune system being able to recognize and respond to the encapsulate organism. These higher affinity IgG antibodies produced will provide better protection than if the vaccine only had the unconjugated polysacchride. 

[1] http://www.vaccines.gov/more_info/types/#conjugate