The Scouring would have only worked as an added bonus segment on the EE-it simply wouldn’t have fit into the flow of the final movie, which already had enough “false” endings.
Too often PJ gets criticized for sins of commission-but there’s a lot he took out that wouldn’t have worked for modern-day audiences, and on top of that there was a lot which had to be trimmed even to fit into the EE’s running time. Some things had to go and in the main he made good decisions in that regard. Do you really want Legolas squealing like a girl when the Balrog shows up? His fearful look said more than mere words would have. We had a few lively hobbit songs, but do you really want to have the film interrupted every fifteen minutes with Frodo or Merry crooning about whatever?
Faramir was redeemed from the point of his change of mind onwards into ROTK. You have to remember that he and his men were under a tremendous amount of stress, but if Book Faramir was in the film it just wouldn’t have worked (“Yeah my kingdom is going to hell in a handbasket, starting with my father, but don’t worry be happy!”).
That said, there are several things which do bug me, some of which have already been mentioned (Scrubbing Bubbles of Death, Denethor, shieldsurfing). But the worst has to be Treebeard and his ludicrous decision not to fight, combined with his cluelessness about destroyed trees in his own forest, and then in a heartbeat he changes his mind, when it had already been established that ents take a lonnggg time to make a decision. In one asinine scene PJ destroys this character 3 different ways from Sunday. My biggest general criticism is that the last two movies were too overpaced, in a similar way to latter-day Simpsons eps-this material demands that you let it breathe, and not choke it with every mad rush from one plot point to another. Fellowship was much more balanced in that regard, but of course PJ would then have to trim even more stuff.
So they’re not the movies I would make, but they are about 90% there, which is good enough for me (even if I have to close my eyes and go “lalala!” at certain points). Perhaps it deserved four films (which we may yet get), tho I’m not sure where I’d make the breaks between them.