A numerical simulation of a two-dimensional rectangular supersonic intake has been performed in a steady-state condition to understand the effect of separation bubble size and its position on the intake performance. Diverse characteristics of separation bubbles in terms of their position, size and quantity have been systematically investigated under varying cowl deflections ranging between $\alpha $ = 0${{\rm{\;}}^ \circ }$ and 4${{\rm{\;}}^ \circ }$ within the intake system. The study encompasses a range of Mach numbers, specifically between M = 1.5 and 3, allowing for comprehensive comparisons of pressure recovery and flow distortions associated with each configuration. The flow field is generated using compressible Reynolds-averaged Navier-Stokes equations along with k-$\omega $ turbulence model. The numerical model is validated using previous experimental and numerical results. Intake unstart is observed when a large separation bubble forms on the ramp surface. The separation bubble shifts from the ramp and moves towards the exit as the Mach number and cowl angle change, resulting in the intake restart. The performance of the intake is observed to be degrading as separation size increases with changes in Mach number and cowl angles. At fixed Mach number, pressure recovery of the intake is observed to be improving with increase in cowl deflection owing to the reduction in net separation bubble size. Maximum TPR of 0.772 is observed at M = 2.2 with 4${{\rm{\;}}^ \circ }$ cowl deflection characterised by net separation of 1.65 mm. Flow distortion is found to be dependent on separation size, position and number of separation bubbles.