When designing an experiment which is the hardest part to design and why

The controls of the experiment. In a well controlled experiment, there are positive and negative controls, and the controls need to show that the experimental results are due to a specific reason and/or experimental conditions, otherwise, the credibility of the results or the causative/ relevance of factors cannot be deduced accurately.

Of course, this is a subjective question and different people might find different parts of the experiment hard to design. This is thus just my opinion.