WiMAX JEEE802.16e standard is proposed as an attractive wireless communication technology for providing broadband access. For the network and application-level capacity and performance analysis, we first provide a short overview on mobile WiMAX networks, and then describe mobile WiMAX PHY and MAC layer. Afterward we present and discuss the benefits and challenges of flat architecture for mobile WiMAX networks. In this kind of architecture the access service network gateway and base stations are consolidated into a single channel. All-IP flat architecture is a promising option. When supporting both voice and TCP in a mobile WiMAX networks, there are two conflicting goals: to protect the VoIP traffic and to completely utilize the remaining capacity for TCP. We investigate the interaction between these two traffics. Finally, we emphasize that TCP variants, priority queues, bandwidth limitation and traffic shaping do not always achieve the coexistence goals.