In Next Generation Air Transportation System (NextGen) operations, we expect that the demand-capacity balance can be achieved by selectively managing the airspace capacity in conjunction with managing the traffic demand. In Flexible Airspace Management (FAM), the airspace complexity can be assessed a few hours ahead in order to identify sectors that could exceed their defined traffic threshold as well as sectors that are under-utilized. Using various airspace optimization algorithms, airspace can be reconfigured to manage the existing traffic demand without moving aircraft away from their original user-preferred routes. A human-in-the-loop simulation study was conducted in 2009 to assess the impact of airspace reconfiguration on the controllers. The results from the objective data found that the acceptability of the boundary change and the associated workload were mainly affected by airspace volume change and aircraft that changed ownership. However, observations and subjective feedback have suggested that other cognitively-driven factors, such as spatial relationships between upstream/downstream sectors, may also play a role, especially in traffic situations where the airspace has only a few aircraft that change ownership but still has a high degree of airspace complexity associated with the reconfiguration. In this paper, we identify these factors and discuss the human factors issues that should be considered in designing the airspace and airspace transitions.