I watched M2 the other day and here's the interesting thing: I REALLY enjoyed the movie. It was something I hadn't experienced with that film before.
UNfortunately QCing M3 I was a bit disappointed with the experince (be aware I'm a bit of a fussbudget). It has a rough cut feel to it. You sort of have to fill in some gaps in your mind yourself. But of course that's really necessary since there is no footage of Trinity getting Neo's body and bringing him back from Zion, etc. Also there's footage I've cut in after the battle of Zion and of course everyone has no healing cuts or anything which seems odd. We can only assume time has passed and they have good medical care (remember Bane cut himself and didn't get medical treatment for them, so he would have those marks.) I'm sort of considering this 'the movie that could have been'. Sort of a concept fan edit film.
I'm sure EtM has great footage, but I've also been told by others that none of the footage would be very useful. The truth is I don't know and I wouldn't go back and add it at the late of a date. If someone else wants to do a super complete Matrix with deleted scenes and EtM cut in, I'd love to see it, but that is not what I'm doing.
The theme is to eliminate anything that seems jarring in relation to the first film (philosophically or tone-wise). Another name for this could be the happy ending cuts. There are fewer dead and a different mood at the end.
I'm going to see about tweaking M3 since maybe it was just me. When watching it (I had really high expectations after M2 came out so nicely).