Are you sure you're using it correctly? Its not particularly intuitive without any written explanation of how it works...
How To:
Define the load-outs you want crew to take in the ship customisation screen, then as a captain you click on the class icon of the player you want to recommend the loadout to (spanner helm or bullet to the left of their name), and the suggestion UI will appear with the three possible load-outs you saved in the ship customisation which you can recommend to that player. You have to recommend a loadout to each of your crew individually.