1) what the ultrasound show? is it simple/pure cyst?
2) how long has your Ob followed this cyst by ultrasound, especially ultrasound done at different hormonal cycles?
3) is there anything else? Did your Ob tested your blood CEA levels?
Without those answers, it is odd to be so aggressive for just a cyst, albeit it is greater than 3cm, for a young patient.
Definately wait to see the infertility specialist and let him/her work it out. Good Luck!