The main difference is mostly about the means to get to the Caliphate. The Salafis adhere to a political theology that views muslims in the West as migrants in enemy territory, a realm they speak of as Dar al-Kufr (House of the Heathen) or Dar Al-Harb (House of War) — as opposed to Dar al-Islam. Salafis openly espouse violent jihad to actualize the Caliphate in Europe and North America, whereas the Muslim Brotherhood concentrates on non-violent activities, believing that violent jihad in the West should be postponed until the day when their demographic numbers will be sufficient enough for a full-spectrum offensive against the infidels.
That difference is irrelevant in Gaza and Iraq, for instance, where both Salafis and the Muslim Brotherhood embrace suicide-bombings and other forms of satanic violence.
That being said, it can be more complicated than that. I mean -- many Salafists in Syria despise both al-Qaeda and the Muslim Brotherhood... More details here.