Recent increase in e-commerce, warehouse operations have become one of the most significant issues. Recent customer profile requests fast delivery time with flexible options in purchasing. Automated warehousing technologies are widely utilized in warehouses to provide fast solutions for those demands. Shuttle-based storage and retrieval system (SBS/RS) is an automated warehousing technology assuring fast transaction process in warehouses. In this work, we study a special design for SBS/RS where automated vehicles (i.e., shuttles) are more flexible in their travel pattern so that the system would not require a dedicated shuttle in each tier resulting with decreased number of shuttles compared to a dedicated one (i.e., each zone with a single shuttle) in the system. We compare these two system designs, flexible and dedicated ones, by using an agent-based simulation modelling approach. The proposed flexible design is developed on deadlock and collision prevention algorithms evaluating real time information. The performance of the system is compared by their average flow time per transaction, maximum flow time of a transaction, throughput rate and utilization of shuttles, etc. The results show that by integrating smart collision and deadlock prevention algorithms, the proposed flexible aisle-to-aisle SBS/RS works better than the dedicated system.