An innovative modular aircraft, called Clip-Air, is being designed at Ecole Polytechnique Federale de Lausanne (EPFL). The novelty of Clip-Air from a transportation system viewpoint is its flexibility due to the decoupling of load and carrying units. In this paper, we analyze the impacts of the flexibility of Clip-Air from the airlines perspective. To quantify the potential advantages of this new system, an integrated schedule design and fleet assignment model is developed for both standard airline fleets and Clip-Air. The model considers spill and recapture effects to represent the demand in case of capacity shortage. Recapture ratios between available itineraries in each market segment are appropriately calculated through an itinerary choice model. The comparative analysis is carried out under different scenarios which are selected with the purpose of understanding the effects of the network structure, fleet size, fleet configuration and the estimated cost figures for the Clip-Air system. It is observed that Clip-Air uses the transportation capacity more efficiently by carrying more passengers with less overall capacity. Moreover, Clip-Air is found to deal better with insufficient transportation capacity. Furthermore, the scheduling decisions are robust to the estimated cost figures of Clip-Air. For the analyzed range of costs Clip-Air is always carrying more passengers with less allocated capacity compared to standard fleet.