It has been a long time since I have made pants of any kind, but I have done it both ways. I want to make pajamas for Christmas gifts, so will probably sew them your way. If I remember right, I think I preferred that way when I tried it. Some of my pajamas will be for men, and my pattern does not show a fly. I would rather not go to the trouble of making a fly, but would that be acceptable? I have two patterns, and neither show a fly. Why would a pattern company even make one that way?