Unless you were conducting a strict thematic analysis where your aim was precisely to identify themes, you should be able to articulate your thematic findings as answers to your research question. If you can’t, then you probably haven’t taken your analytic task sufficiently far enough.
Did you, for example, identify three themes about fatigue management, or did you identify three barriers to the adoption of fatigue risk management policies? In the former, authors usually structure their findings along the lines of ‘the first theme…’, ‘the second theme…’, etc. As a reviewer, this is a giveaway to me that the analytic task has not been completed and that there is a lack of internal consistency between aims, method, findings and conclusions/implications.
Once you can articulate the themes in the same terms as your research question (which is to add another step to your analytic project), then you can organise the order of their presentation in a way that is not only more sophisticated but much more meaningful. It is a subtle shift, but it makes a world of difference to the narrative of your paper. Moving beyond the thematic can test your ability to achieve a more concrete understanding and expression of what you really found.
By way of example, consider the following paper:
We presented our findings as ‘three attitudes that contributed towards stated helmet use’. That provided a much more engaging narrative than if we had just presented ‘three [random] themes about helmet use’. We were then able to layer our findings by pointing out that each attitude had the potential to encourage or discourage helmet use, which led to our conclusion about the importance of contextual behaviour change strategies that countered any unintentional consequences of messaging.
We could have made the same argument just by deferring to ‘three themes’ but that would have been less engaging, less convincing, less confident and a wasted opportunity to demonstrate our ability to analyse data specifically against the aims of the research (ie. the internal consistency of the study).