What questions to investigate
It often takes work to develop a question that is (a) worthy of further study with an investigation, (b) possible given the time and materials available, and (c) can help you make progress understanding the phenomenon.
How to represent the phenomenon
Investigations are, at heart, re-representations of complex phenomena in places and at scales that allow us to study them. Scientists have to decide what aspects of the phenomenon to represent and how to represent them, even before they are entirely sure what is important.
How to develop an informative comparison
Developing an investigation involves deciding what to compare and for what reason. This includes identifying and controlling variables, considering whether a comparison will provide information, and considering scale (e.g. how much to vary a factor to decide if it makes a difference).