Is the ability to generate scientific questions a sort of inclination? This is my 3rd year of PhD in Germany and I don’t hold it yet.

At some point in the process of becoming an independent researcher, one has to be able to come up with one's own questions/hypotheses.

Has your work to date been prescribed by your supervisors? Have you had to develop lines of inquiry based on findings from your work?

This was always one of my biggest worries: how will I ever be able to develop research questions? I have found, surprisingly, that I can and that it just took time to understand the literature directly related to my research question and also the areas that other researchers working on similar topics were addressing. I have only been able to do this adequately as I entered my 3rd year.

Think about the next research questions you would address for your own work after your PhD. If you can't answer this now, I'm sure you will be able to eventually.

My situation is a bit opposite. While reviewing literature, I am coming up with a lot of research questions and I am finding it difficult to narrow down to a few. However, thinking of research on these problems and any solution is a bit difficult part for me. Trying to figure out how to go about it?