For my edit of AOTC, I amalgamated other editor's ideas for the various plot threads, largely operating as a curator.
I more or less mimicked Slumberland for the romance plot. He carved out a nice little bit of characterization early in the film for Padme. She refers to Anakin as a child when they meet, then points out that he's grown up before leaving together. He also converted the lakeside kiss scene into a day-for-night replacement for the fireside scene, though he inexplicably included Padme pulling away from it.
I retained a truncated version of the "forbidden love" angle. It is hinted at that Jedi aren't supposed to do that, but it's not expressed as being strictly forbidden necessarily. It's enough to get the audience to understand (and remember through to the next film) that the two of them need to keep it a secret. (And hopefully the sequel trilogy depict "New" Jedi who are free to marry and procreate, and retcon the PT such that only the latter Jedi were so conservative.)
I used part of Secior's idea for Count Dooku. Seciors moved his meeting with Sidious to the front of the film and made it much more clear that Dooku is working for Palpatine by trying to assassinate Padme. I did not reorder that particular scene, so Dooku does begin as a ""mystery"" in my edit as in the theatrical version, though we do find out that Palpatine's behind it all (rather than Nute Gunray demanding Padme's head out of pettiness).
I lovingly borrowed many ideas from the good 'ol Phantom Editor, including his method of removing some of the ""mystery"" plot thread about the toxic dart, and the general order of scenes during that part of the film.
Two small things: I changed the recurring mention of "ten thousand" Separatist systems to merely "one/a thousand," because I feel it alienates the audience a bit less. Incredibly minor, though. I also removed many of the Jedi's commands to Clonetroopers during the battle, implying that the Jedi are going to become dependent upon them during the war.
That's my take on Episode II, following in the textual tradition of fan editing and making use of what others have done. As always, I edit because I want the end product to exist.