Guras, let's face it, community in Skirmish is already strongly separated into clans. Vets rarely play with people they don't know on their ships.
In Alliance community is already split apart into factions, so there's no changing that. On the other hand if I want to help my faction (find my faction's match) then I want to find my faction's match, and for that I can communicate more with my faction mates. Imagine factions as bigger clans except with some actual fight for power and effect in game, even if it's only colour on the map.
I honestly don't see your point. For me it would be fun to be able to plan and strategise together with my faction and it would actually enhance the community (because at least I cooperate with my faction instead of just playing with my clan and friends).
Edit: well I don't know if faction system is going to end up in skirmish, so I assume it won't, but yeah, it would be cool to have sth similar in skirmish, perhaps with clans or just, dunno, Red vs Blue thing.