It seems like docs are more familiar with clomid, that's all really.
Femara works well for women that don't ovulate with clomid. So, if you still don't ovulate on clomid, I'd ask for femara next time.
I used clomid in the past and it thinned my lining and gave me a cyst. Doc thought femara would be a better choice for me. It didn't thin my lining, and I'm due for an ultrasound later in the week to check for cysts.
Having done both, I'm not sure which I prefer. They both gave me hot flashes. Clomid thinned my lining, gave me a cyst, and I gained 10 pounds after 4 cycles.
Femara gave me a headache for 10 days straight though.