From our perspective, so what? Both sides regard the West as the enemy to be conquered. Their differences are germane only to the extent that sharia fidelity, in addition to sheer brute force, will determine who comes out on top in their intramural warfare. As we have been observing here for years with respect to al-Qaeda and the Brotherhood, their disputes are mostly tactical; their splits on the finer points of Islamic-supremacist ideology bear only on how they regard each other. When it comes to the West, both see us as the enemy — and they put aside their differences to attack us.
The same has also always been true of the ideological/doctrinal divide between Sunni and Shiite jihadists. For example, al-Qaeda has had cooperative and operational relations with Iran since the early 1990s. Iran collaborated with al-Qaeda in the 1996 Khobar Towers attack that killed 19 U.S. airmen; probably in the 9/11 attacks; certainly in the aftermath of 9/11; and in the Iraq and Afghan insurgencies. Al-Qaeda would not be what it is today without state sponsorship, particularly from Iran. The Islamic State might not exist at all.
The point is that al-Qaeda has never been anything close to the totality of the jihadist threat. Nor, now, is the Islamic State. The challenge has always been Islamic supremacism: the ideology, the jihadists that are the point of the spear, and the state sponsors that enable jihadists to project power. The challenge cannot be met effectively by focusing on one element to the exclusion of others.