The decision whether to go for a frequency domain analysis or a time domain analysis is not straightforward, and there are some main factors you should account for. I will try to summarise, but beware they will not be enough to assure anyone that the "best" approach will be attained.
Often, frequency domain analysis cannot be replaced by a time-domain analysis, when you know, or expect, or are required to verify whether the structure will respond dynamically with the excitation load frequency (like aerolastic structures, wings, blades, tall buildings, towers, bridges, pipelines, risers and structures subjected to VIV or resonance with local machinery like vehicles, ships, steel frames, machinery foundation, acoustic loads...). If one decides to work in the time domain with these types of structures, one might overlook any dynamic amplification factors and will get a wrong expected life (wrong cumulative damage, wrong stress cycles) and maximum expected stress might be significantly off (low RMS stress, low peak stress, wrong stress ranges).
In the frequency domain, you must feel confortable working with load spectrum, mode shapes, response analysis, harmonic analysis/transfer functions, linearizations, statistics, damage computation methodology, damping factors and simplified equivalent models to keep the analysis reliability under control.
In the time domain, usually one will be working with large load data, that will require significant computational power and labor, but one might feel more in control of the analysis process and routines. Complex problems can be verified directly in the time domain, whether the frequency domain analysis usually requires simplified models (beam models, equivalent models, analytical models) to get the results within schedule, specially with changing designs. Sometimes, a time-frequency hybrid analysis is more indicated to let one benefit from both the time domain capability of working faster with complex shapes\structures, and from the frequency domain capability of verifying global and local dynamic responses under random or harmonic excitation loads, in these cases FFTs are applied to translate from one domain to the other and back again, retaining reliability.