The present paper concerns the individualization of the training of aircraft pilots. Specifically, it presents the data collection, and modeling efforts carried out to assess trainees' transition from a controlled, effortful piloting experience (i.e., System 2), to an automatic, effortless process (i.e., System 1). It is argued that cardiovascular activity can be associated with deployment of effort, and therefore be used for assessing the transition across systems. Heart rate, respiration rate, and heart rate variability were sampled on 11 pilots (5 students "novice" and 6 instructors "experts"), performing 6 one-hour flights (5 flights in tandem: one student and one instructor, the 6th flight with an instructor flying alone). These data were used for the development of a prediction model computing the probability of a pilot being an expert or a novice. After a "leave-one-tandem-out" validation, the accuracy of the model was 86.86%. The results are discussed in terms of effortful processes and skill acquisition. Further work will consist in implementing contextual parameters in the model in order to improve the prediction. Such a model could be used by instructors and trainees as a supporting tool for tracking progress of the training at the individual level.