Well, Mcquarrie wrote Ghost Protocol,
But, I am sure Cruise wanted that connectivity, too.
Yeah I have a feeling it was McQuarrie (and Cruise). Though he is strangely uncredited for GP, Cruise has made no secret that McQuarrie was at the very least A writer on it and that's where their partnership on the series was truly formed and they made all these plans. So it makes sense that they'd be the ones creating that connective tissue from MI3.
I always think of MI3 as the prototype or first draft of the franchise that became fully formed in
Ghost Protocol. It's like, Cruise knew what direction they wanted to take the series in tonally, they knew they wanted to stress the team element more, the pieces of the team dynamic were
starting to take shape, but it just wasn't quite
there yet. It was the Abrams version of Cruise's vision for the series, basically. Which came across a bit more like a high budget episode of
Alias with Cruise instead of Garner, but still pretty close to what Cruise wanted. But yes, to me, that film was basically the first installment of what the franchise is now. The first M:I has its charms (I'm actually watching it right now), the 2nd one...less so, but they bear little resemblance to the series from III onward. If you are new to the series, you can totally just start with MI3 and not really miss a beat.