I agree with one thing: both al-Qaeda and the MB in its various incarnations have the same broad goal - an Islamist state that governs principally by sharia law. AQ probably envisions this state covering all the old domains of the Umayyad caliphate + Central Asia and East Africa, while the MB's mental map doesn't go quite so far, but one should never, ever forget that the MB are Islamists.

I very much doubt, however, that the MB/AQ are like Sinn Fein/PIRA. More like the Communist Party of India (Marxist), which governed West Bengal and Kerala for decades, and the Red Army Faction. Both fly the Communist flag, both probably envision a state governed by Communist principles - but one participates in government more or less peacefully, while the other principally enjoys bombing people and issuing communiques - and neither in communication or control of the other.