Turbulence and flow disturbances occurring at the aircraft wing-fuselage junction cause a deterioration of its aerodynamic performance and an increase in the aircraft's drag force. However, the aircraft junction regions are currently designed empirically due to the lack of knowledge of detailed junction flow dynamics, which consequently leads to less efficient flow management and poorer aerodynamic characteristics. The main objective of the present mathematical-modelling study is research on an aerodynamically enhanced design approach, concerning the improvement of the characteristics of the junction flow and its vortices. Numerical simulations are performed under the prism of vortices' structure formation and patterns, particularly of the horseshoe and corner separation vortices, which dominate such flows. More specifically, this research study proposes a new junction flow parameter, which has been employed in combination with the existing ones, in order to result in a more streamlined and efficient junction design, and investigates the junction flow response, when the reference junction design of a wing-fuselage system is modified by the addition of "fillet", "strake" and "blending" geometry types on the wing. Flow simulations are performed in steady-state mode, at transonic flight regime and at 2° angle of attack, using two turbulence models: The Reynolds Averaged Navier-Stokes (RANS) SST k-ω turbulence model, enhanced with rotation/curvature corrections (SST-CC) and with eddy viscosity and turbulence production limiters, and the second-order closure Reynolds Stress model. The geometrical modifications that were implemented proved to be efficient and their application in the design process of modern aircraft foreshadows the possibility of achieving enhancedperformance flights. More specifically, all the three modifications of the reference geometry increased the aircraft's aerodynamic efficiency, by improving the flow pattern around the wing-fuselage regions at the studied flight state. The most promising configuration proved to be the one which combined the "fillet" and "strake" geometries, resulting in the highest aerodynamic efficiency, by greatly weakening the horseshoe vortex and eliminating the corner separation.