As the scale of system integration continues to grow, the on-chip communication becomes the ultimate bottleneck of system performance and the primary determinant of system architecture. In this paper we propose a throughput-driven synthesis methodology for on-chip communication fabrics based on optimized bus models. Compared with traditional delay-driven, wire-by-wire planning methods, the throughput-driven methodology provides a feasible and accurate system-level solution to address delay and congestion problems simultaneously during early-phase design planning. Unlike the conventional methods which are based on rather inaccurate RC models and simplistic delay metrics, in our methodology the communication fabrics are characterized in terms of realistic Partial Element Equivalent Circuits (PEEC) extracted from the multi-layer interconnects and transistor level transient analysis via SPICE-like tools. The characterized models facilitate a flexible interconnect fabric optimization engine that can be embedded into a system planner for throughput-driven synthesis. Furthermore, engineering trade-offs considering repeater area and interconnect power consumption are further considered as part of this methodology.