I mentioned an idea about this before.
Keep the 3 man fireteam limit, but make it so that the people you are instanced with have different priorities.
First: Friends
Second: Clan members
Third: Everyone else.
Now we could take this a step further and say you are both in the same area but different instances. You select them from your friends list and hit join instance.
Just one way you could play with your friends even if you're not in the same fireteam.
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The way Bungie are pushing Clans, I think they would have #1 priority.