I am very impressed with the visual rendering, and the comparison video you packaged with the edit proved educational and were reminscent of the TF Movie DVDs I picked up in 2007 which boasted similar features.
On a narrative level, the story is very clear and both Optimus revival episodes compliment each other well, I quite like how you synched up Optimus's suicide mission with his rescue. Being an editor I have often wondered if one could skirt around showing the crisp and clean looking Optimus the whole time the rescue mission was underway, but watching it with it fresh again in the memory I can now say that would prove monumentally difficult. Obviously the continuity gaffs can't be avoided, but the storyline still works.
There were instances where I feel the traditional Autobot/Decepticon logo flips would have provided better transistions than some abrupt cutaways and transistion fade-ins, the sequence following Prime being revived for example is quite sudden, as is a scene from earlier which switches from a sun to the moon (visually that's great, it's just the audio cut that sticks out)
Also, did we need to have a recap of the story so far half-way through the movie? I know Optimus needs to be brought up to speed, but we as the viewing audience certaingly don't. I think this could have been easily skipped.
There is plenty to enjoy in this omnibus, and it was good to revisit some of these really solid run of storylines and characters, combined with a firm restructuring of the visual specifications, I would still recommend viewing this edit even if I have a feeling it's only a few steps away from being truly refined