I haven't seen this fanedit yet (can't wait!), but everything sounds awesome so far, and the cover art is brilliant. I am a big Transformers fan being a child of the 80s, but I admit that I know little. My biggest gripe with the movie is Starscream. What the fuck? I always liked how Starscream looked as if he had angel wings, but now he's a huge triangle with little stubby legs. And why couldn't his head have been more accurate like Prime's? Oh yeah, Megatron should have been a tank, so he could have that huge blaster cannon (which made an awesome blast sound in the cartoon). Anyways...
I hate Linkin Fart, but I actually liked that finale song except for the heavy rock guitars in the credits (if I remember correctly). I think your attempt at changing the song was a good try, but you lose most of a good monologue that sums up the movie well. You could cut the small kissing shot out to fill some of that empty space. (Plus, it somewhat doesn't go with sad music you've applied anyway, unless it's supposed to be ironic.) Since you don't have Prime's dialogue by itself, maybe you could check out an audio book, or a version of the movie that has 6.1 or 7.1 sound. I don't know if these versions exist.
If the soundtrack is messing with your true vision, I say "fuck it". I was thinking that you might be able to cut and paste parts of the song and fade it out. What I mean is, find where a measure of a song ends and paste in a previous part of the same song, so it repeats enough times that you can fade it out in the next scene. This way you don't end up with an abrupt ending to the music when you cut something. However, this may be impossible, because you have to worry about sound effects and dialogue getting in the way. Maybe you could use the actual soundtrack for this instead.
I've used Sony Vegas a lot, so let me know if you need a little help. If you fade out a track and right-click the fade-out, it will give you options like "slow-fade" or "fast-fade" which should come in handy. I also like the "cross-fade" feature. If you overlap 2 audio tracks, it will automatically do a cross-fade for you. This just means that the first track fades-out while the other one fades-in.
I'm really looking forward to the Generation One version of this. Hell yeah! I really like someone's idea of using the old lazer sound effects. With all of the effects manipulations in Vegas, you could come up with something that sounds like a cross between a laser and a machine gun. I love the music from the old cartoon, but I'm afraid the hair metal music from the animated movie (like the theme and "You've Got The Touch") would add cheese back into the movie. However, the animated movie has some gems like "Unicron's Theme" even though some have that BIG 80s reverb on the drums (not a big problem though). It would be cool if you could find some good remixes of the cartoon music on the web.
P. S. Keep up the good work! Thanks for making this movie so much better. By the way, Transformers Rifftrax is fucking awesome!