The design of integrated circuits presents an increasing challenge for engineers, who seek to identify effective methods for cooling the miniature electronic components that are becoming increasingly complex. One potential solution is the use of micro pin-fin heat sinks, which have the potential to be an effective thermal management technique. This study compares the potential thermo-hydraulic efficiency of micro heat exchangers with conical pin-fins, arranged in two alternative patterns. The flow topology was investigated using the critical points theory and Ω-criteria to gain a deeper understanding of vortical structures and flow separation. 75 variations of pin-fin arrays were simulated and analyzed. It is noteworthy that no pattern similar to bidirectional pin-fins has been studied previously. The input datasets for the simulations included pitch/height ratios ranging from 0.823 to 1.235, cone angles from 0° to 13.48°, and flow Reynolds numbers of 40–117. The numerical results show that Ω and kinetic energies can predict the onset of instabilities. The degree of conicity and the pattern affect the friction factor, typically reducing it. The conical shape and arrangement of pin-fins can also aid in stabilizing the flow. Furthermore, the dependence of the friction factor on pitch/height and Reynolds was quantified with the calculated mean relative error of 1.7%. Moreover, turbulence parameters and friction factors were used to evaluate the thermohydraulic properties, deliberately excluding heat transfer simulations. This approach allows a much wider range of geometric modifications to be investigated for the preliminary optimization of the thermal and hydraulic performance of microchannels.