So I'll be the first to say I'm not real informed on the purpose of Fleet Carriers. I know two things really; they're expensive and the jump real far. At first glance they seem ideal for explorers looking for a mobile home but are way too expensive to upkeep for the lone explorer (I think) and outside of that I can't think of any other purpose they serve in the current game. Which leads me to my point, I think they are being introduced to support gameplay that has yet to arrive.
Without getting too into the weeds about everything they could be I hope they intend to add some sort of Eve Online-esk faction wars. I think it'd be really cool to see them fill the same role as Capital ships from Eve supporting massive war efforts. All that they would need to introduce is a version of player factions similar to that of Eve Corporations allowing player owned factions to war with other player factions. I imagine 2 or 3 fleet carriers warping into an opposing factions space (at a designated time for both sides so each faction could prepare) and with multiple fleet carriers for the other faction following suit. Combat with 50 to 100 players with multiple wings coordinating defensive and offensive maneuvers.
This is likely not the case but I'd be interested in hearing opinions on this or if you think something else entirely may be coming or even nothing at all.