Manufacturing systems are crucial for the Industry. A frequent objective is therefore to improve the throughput of the system, which can be done by allocating buffers in the system or by improving the machine performances. Yet, while an increase in the buffer size usually increases the throughput, it often also increases the inventory and the makespan. Furthermore, improving the wrong machines will only incur cost but not improve the system performance. This paper describes a general prediction model of these performance measures for different buffer allocations and machine performances based on only a single simulation using a holistic approach.