Despite the evolution of unmanned aircraft systems (UASs), the technological development on airframes, autopilots, communications and payload, is still limited by the absence of software standardization. Engineers face the development of UAS systems with the implementation of ad - hoc solutions to satisfy the mission requirements. This is a major limitation with regard to the software maintenance and re-usability that may result in an increment of both project cost and risk. Wellstructured UAS avionics supporting increased levels of automation (and eventually autonomy), together with reconfiguration capabilities and costeffectiveness, are key requirements for UAS to be successful in a global scenario. Additionally the major civil applications require UAS with access to non-segregated airspace. Following Eurocontrol, FAA and ICAO philosophy, the introduction of unmanned traffic should not affect ATM operations, thus UAS should comply with the performance levels required by SESAR and NextGen. Hence, operations with unmanned aircraft should guarantee safe and efficient interaction with the ATM system. In that aspect gaps and issues into unmanned aircraft software architectures are discussed in this paper. Required mechanism for ATM communication, collision avoidance, maneuver automation and SESAR/NextGen integration are discussed to identify possible short-term and long-term software requirements. Moreover, existing standardized software frameworks and proposed software proposed are reviewed to identify the gaps it should deal with to achieve an efficient UAS integration.