Human-swarm interaction (HSI) involves a number of human factors impacting human behaviour throughout the interaction. As the technologies used within HSI advance, it is more tempting to increase the level of swarm autonomy within the interaction to reduce the workload on humans. Yet, the prospective negative effects of high levels of autonomy on human situational awareness can hinder this process. Flexible autonomy aims at trading-off these effects by changing the level of autonomy within the interaction when required; with mixed-initiatives combining human preferences and automation's recommendations to select an appropriate level of autonomy at a certain point of time. However, the effective implementation of mixed-initiative systems raises fundamental questions on how to combine human preferences and automation recommendations, how to realise the selected level of autonomy, and what the future impacts on the cognitive states of a human are. We explore open challenges that hamper the process of developing effective flexible autonomy. We then highlight the potential benefits of using system modelling techniques in HSI by illustrating how they provide HSI designers with an opportunity to evaluate different strategies for assessing the state of the mission and for adapting the level of autonomy within the interaction to maximise mission success metrics.