1.75 or 3mm, for a Bowden setup?
1.75 takes less force to extrude, but commensurately cannot transmit as much force. Also has a higher tendency to buckle under stress, and increased issues with ooze.
3mm has less issues with buckling and retraction, but requires greater force to extrude - increased stress on the components. Since it’s Bowden, I see no problem with increasing the stepper size to compensate for force/speed issues.