Many unmanned aircraft applications require or benefit from deploying a fleet to perform a mission. Technology innovations such as rapid prototyping and microelectronics enable the use of unmanned aircraft systems (UAS) at lower costs, so the ability to design a bespoke UAS for a specific mission is an additional advantage. The problem of designing the new UAS and allocating the fleet of these aircraft is a challenging optimization problem. Using constrained multi-objective design optimization with an interactive multicriteria decision-making method, which involves the mission customer, the approach in this paper generates UAS designs and fleet allocations and determines preferential solutions for the customer. The paper presents a case study involving a UAS weather profiling mission for the aircraft sizing and fleet allocation and uses inputs from meteorological subject-matter experts acting as customers to demonstrate the functionality of the approach.