Evaluating the performance of complex systems, such as air traffic management (ATM), is a challenging task. When regarding aviation as a time-continuous system measured in value-discrete time series via performance indicators and certain metrics, it is important to use sufficiently targeted mathematical models within the analysis. A consistent identification of system dynamics at the evaluation level, without dealing with the actual physical events of the system, transforms the analysis of time series into a system identification process, which ensures control of an unknown (or only partially known) system. In this paper, the requirements for mathematical modeling are presented in the form of a step-by-step framework, which can be derived from the formal process model of ATM. The framework is applied to representative datasets based on former experiments and publications, for whose prediction of boarding times and classification of flight delays with machine learning (ML) the framework presented here was used. While the training process of neural networks was described in detail there, the paper shown here focuses on the control options and optimization possibilities based on the trained models. Overall, the discussed framework represents a strict guideline for addressing data and machine learning (ML)-based analysis and metaheuristic optimization in ATM.