In this paper, we compare two trajectory-centered Air Traffic Flow Management (ATFM) architectures that assign a trajectory and a departure time slot to each flight. The main feature of these architectures is the use of trajectories that are feasible from the operational point of view and are aligned as much as possible with airspace users’ preferences. The first architecture is inspired by the first-come-first-served principle and can be seen as a proxy of the approach currently used in practice. The second one—herein named “preference-aware ATFM architecture”—considers alternative trajectory options and explicitly takes the related preference scores into account: its main objective is to provide better trade-offs between user-preferred trajectories and system efficiency. The analysis herein carried out highlights the benefits of the latter architecture in terms of both system efficiency and satisfaction of airspace users’ preferences, thus paving the way to its potential use as a tool for the ATFM collaborative decision-making process.