Based on my experiences, the Smugglers Run single rider line almost always results in a much shorter wait, but you can't choose your position, which means you'll almost always end up as an engineer. You always have the option of asking someone in your party to switch roles, but you can't request a specific role from the loading CM, which is an option if you go through the traditional standby line.
Also, while the Flight of Passage single rider line doesn't get used in the traditional manner, you can identify yourself as a single rider when you reach the FP/standby merge point, at which point you'll be put into the middle line, where they pick single riders to fill the 16-person room if needed. If you have a FastPass, I don't recommend this, since that will probably get you into the room faster than the single rider option, but it is a good option if you're standby.