We present an integrated schedule planning model where the decisions of schedule design, fleeting and pricing are made simultaneously. Pricing is integrated through a logit demand model where itinerary choice is modeled by defining the utilities of the alternative itineraries. Utilities are explained with the fare price, departure time and number of stops. Spill and recapture effects are incorporated in the model to better represent the demand. For the recapture ratios we use a logit formulation similar to the demand model so that the ratios are determined by the model according to the utilities of the alternatives. Furthermore fare class segmentation is considered in such a way that the model decides the seats allocated to each fare class. To deal with the high complexity of the resulting mixed integer nonlinear problem, we propose a heuristic algorithm based on Lagrangian relaxation and sub-gradient optimization. The study is in the context of a project regarding the design of an innovative air transportation system called Clip-Air which has flexible transportation capacity. In order to quantify the potential advantages of this new system, models are extended to work with Clip-Air fleet and comparative analysis is carried out using a dataset for a major European company. It is observed that, the enhanced flexibility of Clip-Air allows to transport around 15% more passengers with the same overall fleet capacity.