A question often asked is “which options work best” to which the answer is always “it depends”. This is primarily because the outcome of the analysis depends more on the quality of the data than anything else. However I would always try for yourself and get a feel for how the program works for your data - running both pipeline=dials and pipeline=3d will simply require more computing time / disk space rather than more effort, so it is certainly worthwhile. For small molecule data though pipeline=3dii small_molecule=True is a good mix.