Hi preggers and welcome!
Congratulations on your soon to come baby! I never gave birth so perhaps others can help you more than myself. Logically thinking, I tend to think that giving birth naturally would be better compared to a C-Section. Less stress on your body and probably less time to heal.
Again, I'm not on expect on giving birth.
As far as feeling fatigue, etc., did you detox when you were recovering? Most people don't think to detox which in my opinion is so important to get totally better. In the "New To Lyme? Start Here!" Sticky Thread on top of this forum there are instructions on detoxing. If toxins are not removed from the body they get recycled back into one's blood stream and cause problems.
I have heard that pregnant women should NOT detox because the toxins can get into the mother's breast milk which in turn would be fed to the baby.
Good luck to you whatever you decide!