I am currently on the clomid path and heading toward the FSH/HCG option if we don't get success soon. Yes, there is a chance of CM changes and alteration in the endometrial lining but this is usually after a few cycles. The cost of clomid is less and it is the easier option (tablets for 5 days compared to injections) but it does depend on your specific issues. The endometrial lining can be monitored through U/S and natural therapies like acupuncture can increase CM too.

Good luck.