This is a really good question! I'm glad someone is bringing up this topic.
Unfortunately, I would have to say... nothing. I joined one of each faction so I could get their gear. That's pretty much it. The factions in the game have been criminally underrepresented in the story. Bungie set them up to have such a big part in Destiny, with all the lore about them fighting to take over the Tower and possibly coming back to finish the job and the friction with the Vanguard, but it all just went...
... nowhere.
So, yeah... I don't feel anything about them other than I'm glad they helped me level up. Wish I could say more, honestly.
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Ding ding ding. We have a winner.
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Heavily agree.
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I think you summed it up factions like a lot of little pieces in destiny have such a great impact on the game however due to time or transition from story board for destiny to the actual end game they went no where