Unless the dr is seeing something unusual in your case, I wouldn't think your chances are "slim" There are many of us here with j-pouches who have had children. Some have needed fertility treatments, some haven't. I have three friends with pouches who do not visit this site who had children without fertility treatments. I had four surgeries - two for j-pouch, one to disconnect and one to remove. I did need IVF but I have two kids ages 7 and 4 1/2.
If I were you I would ask the dr for more information. What makes him think the chances are "slim?" A j-pouch alone should not cause this statement.
All that said, Sharon is right. If you need the surgery, you need the surgery, regardless of what might come from it. However, you have options. J-pouch, ostomy, k-pouch, etc...so do your research and question the drs a LOT so that you can make an informed decision. This is a big deal and you are old enough to make choices that will affect your future. Just be sure you have all the information and can make the decision with your eyes wide open.