Updated changes for the DVD Release:
1. Ok, I feel really pissed off at myself for not catching this sooner than I did....

Apparently in two of the "Soundwave in space" scenes (1st is where he acknowledges Wheelie to follow Mikella and 2nd is when he tells the Decepticons to mobilize), Michael Bay - in his efforts to constantly reuse as much footage as possible in TF2:ROTF - used THE EXACT SAME ANIMATED FOOTAGE OF SOUNDWAVE IN BOTH SCENES!!!
http://www.vimeo.com/7551430

(the only difference to these scenes, apart from Soundwave's dialogue, is Wheelie's subtitles in the 1st scene and a slight contrast filter in the 2nd scene)

Repeat footage in movies tend to annoy me to no end (unless it's like in a flashback), so I've gone back and re-edited the Soundwave's "achknowledge" scene in my fanedit to use different footage instead (I've also replaced the "zoom-in from space" shot from earlier in the hacking sequence with an alternative shot of Soundwave):
http://www.vimeo.com/7551456

2. Cut the hacker girl and her black friend from the helicopter scene with Sam/Mikella.

3. Trimmed about 20 seconds from the "Shanghai" epilogue (cut more footage from the Commander Center, removed Captain Lennex and co. talking in the helicopter, and removed Ironhide's "I smell him" line)

4. Smoothed out several music cuts/transitions that could've been better