Should I present future research directions in a separate section while writing a scientific paper?
Anything is Okay. I have seen the future directions in both ways: mostly I found it in the related section, however it is rare in a separate section. So choice is yours. But keep one thing in mind. Your future direction should not be too long unless your presenting results and discussion are enough to be accepted by the reviewers. Otherwise, reviewers of your paper may feel the future directed works are important part in your present paper and may give a comment like "why didn't you conduct same work for this paper?"