Two imidazolium cations containing a benzyl group, 1-benzyl-3-methylimidazolium and 1-benzyl-2,3-dimethylimidazolium, generally produce the large pore zeolite MTW when used as structure directing agents in the synthesis of pure silica zeolites by the fluoride route. When working at low water contents only the smallest of these cations is able to crystallize MFI, a zeolite with crossing medium pore channels. In that case, MFI is metastable towards MTW, but the in situ transformation slows down as the water content is decreased. Structure-direction is discussed in terms of hydrophobicity, flexibility and size of the cations. A conformational analysis shows that the bulkier 1-benzyl-2,3-dimethylimidazolium is slightly more rigid than the smaller 1-benzyl-3-methylimidazolium, and thus could have been expected to depart more easily from crystallizing a default structure such as MTW. The different performance of both cations is investigated by molecular mechanics and the simulations show that the small increase in size brought about by a methyl group at position 2 of the imidazolium ring prevents an adequate sitting of the cation at channel intersections with the imidazolium ring close to the small cavity in which fluoride resides in MFI. The calculated interaction energies help to understand the phase selectivity and time evolution experimentally observed with both cations.