How about some actual interactions with the factions?
Maybe some Faction Wars that take place like Battlefront?
FWC wants to collect a piece of Vex wreckage, but Dead Orbit wants it too, for there own ends. A battle ensues. If you're with DO, you try to stop FWC.
Maybe even a massive Vanguard vs DO vs FWC vs NM kinda battle. Epic.
Make our alignments with them matter. They need to mean something. Make them actionable. Have consequences for my choice to be with FWC or DO...
And for Pete's sake, let us rank them up like we did in Y1...
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That's a mechanic I know of, since TES Morrowind. It would also make perfect sense, as this is a social game. You could actually make a huge guardian PvP event (like 64vs64 plus some AI combatants) out of something like that as well. Depending on which faction wins more of these matches, it would have a real impact on the story.