In this paper, we investigate several properties of the modulational instability (MI) and rogue waves (RWs) within the framework of the generalized fractional nonlinear Schrödinger (FNLS) equations with rational potentials. We derive the dispersion relation for a continuous wave (CW), elucidating the relationship between the wavenumber and the instability growth rate of the CW solution in the absence of potentials. This relationship is primarily influenced by the power parameter σ, the Lévy index α, and the nonlinear coefficient g. Our theoretical findings are corroborated by numerical simulations, which demonstrate that MI occurs in the focusing context. Furthermore, we study the RW generations in both cubic and quintic FNLS equations with two types of time-dependent rational potentials, which make both cubic and quintic NLS equations support the exact RW solutions. Specifically, we show that the introduction of these two potentials allows for the excitations of controllable RWs in the defocusing regime. When these two potentials become the time-independent cases such that the stable W-shaped solitons with non-zero backgrounds are generated in these cubic and quintic FNLS equations. Moreover, we consider the excitations of higher-order RWs and investigate the conditions necessary for their generations. Our analysis reveals the intricate interplay between the system parameters and the potential configurations, offering insights into the mechanisms that facilitate the emergence of higher-order RWs. Finally, we find the separated controllable multi-RWs in the defocusing cubic FNLS equation with time-dependent multi-potentials. This comprehensive study not only enhances our understanding of MI and RWs in the fractional nonlinear wave systems, but also paves the way for future research in related nonlinear wave phenomena.
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