It's hardly limited to this specific circumstance, but why do so many people say "there's only one possible reason for [thing]"? I'd totally dig more character slots, not a single one of which would be for trolling or griefing, I never let myself get bored enough to break Rule #1*. Saying such a thing says more about the one saying it than about the topic, I think.multiple cmdr slots would only have one purpose: Do as much trolling as you can do without taking the penalties for the main cmdr.
Possible other reasons might include:
Different alignment with greater powers (Fed / Imp / Alliance)
Trader / Pirate / Paladin
Different powerplay faction
Open / solo / messing around with mates in a private group / socialising in safety in Mobius
Yes, you can do all these things with one commander slot, especially if you're on the left end of the scale from *Space Deathmatch <-----------> Starpilot RP*. I'd guess I'm far from the only one who doesn't want to do so.
*Rule #1: Don't be a .