On the other hand with Chris laying out exactly why certain story beats and ideas being added made prior ones redundant or pointless and thus cut certainly helps filter out a lot of stuff you instinctively go "They shoulda kept that in!" without realizing how it changes the final film's overall structure.
Yeah, absolutely. There's really only a few minor things I think should have been left in, and even one of those I absolutely see *why* they did it (the original death of Ultra Magnus, just because it's obviously animated to lead up to it, and it makes his resurrection make a bit more sense as he's really just pulled apart rather than being shot to death and it has a bit more internal logic as to why he could be fixed and Prime couldn't).
(The other two are Kup escaping the Quintesson bonds because Hot Rod put his shoulder apart incorrectly, which I think is nicely set up and it's a shame, and how the original script calls out a bit more about how Autobot City is a big energon generation facility and that's why they have all the energon cubes. They could have sold that a bit more while Daniel first looks on the city. But those can stay because they don't affect the pacing and are basically just direction decisions.)