I think you're seeing what you want to see with the framing. In the 16:9 version, even the opening shot is hampered by losing so much of the top and bottom of Unicron as he passes by. I went back and put the 16:9 version in earlier (already watched the 4:3 disc last week) and I think the 16:9 version looks noticeably cramped much of the time compared to the 4:3 version. Most noticeably, characters often have no headroom in the 16:9 shots, sometimes getting part of the top of their head cut off, which you never want to do unless it's for a specific reason. A lot of shots work well in 16:9 but overall the film has a claustrophobic look to me in that ratio.
For instance, here Bumblebee has no headroom at all. His horns are crashing the top of the frame, which is not at all a conventional way to frame a shot like this. His hand is also breaking frame at the bottom of the screen in an awkward way. It's weirdly confining.
Compare to the 4:3 version, which is more open and gives Bumblebee proper head space, appropriate for the shot showing the two kid-friendly characters from the show in a positive and upbeat scene.
Here we have Megatron popping out of frame in his dramatic closeup, which might be intentional but if it were I'd think it would be closer in. You'd want to push further in to cut more of his head off to indicate it was an intentional choice and to create a more "you can't get away from him" feeling.
The 4:3 version shows his whole head, while still cutting off his gun barrel to keep it close in and with him filling the frame to get the point across. In addition, the 4:3 shot gives a better overall impression of Megatron being very badly damaged, lending credibility to Prime's big punch laying him out in the next shot.
Some more examples of what I'm talking about in terms of the 16:9 version being unintentionally confining or claustrophobic:
Hot Rod's head bumps the top of the frame for no reason.
Megatron's head goes out of frame for no reason.
Megatron bumping the top of the frame again.
And again.
Ratchet's firing pistols, the primary foreground action of the shot, repeatedly break the top of the frame, meaning we can't even see the laser being fired, which would qualify as a special effect and thus cost extra money. There's no way this would be covered up if it didn't have to be.
And perhaps most damning of all, the big moment of the film, Optimus Prime's death, is absolutely staged with a 4:3 frame in mind. There are numerous ways this could have used the widescreen format, but instead this is a very vertical shot, with Prime almost fully upright in the frame. It's so vertical that Magnus and Hot Rod are crashing the top of the frame, although to be fair Magnus is so tall and so unimportant to the focus of the shot that this is incidental. But there's no inherent reason to position Prime and everyone else like this. I think it's telling that the key emotional punch scene of the film shows almost no interest in the wide framing at all.
Comparing the two versions gives me a strong impression that Shin was more comfortable in the 4:3 ratio but had to work with the 16:9 ratio as best he could. Some of the shots are inspired and really take advantage of that framing, but a lot of them are also made more awkward or badly framed by it, too. In the end, I will probably default to the 4:3 version more often than not, and I would think that since 4:3 is the ratio Sunbow expected it to be seen in most often (probably forever, given that it was planned to have far more longevity as a TV rerun and a VHS release than as a theatrical release), that's the one that was favored in terms of framing overall. Most kids who were fans saw this once in 16:9 and probably a dozen times 4:3, and Sunbow knew that was going to be the case. I maintain it was primarily directed with that in mind, while attempting to just make sure most of it fit in the widescreen framing adequately.
And of course let's not forget that we're probably
both wrong to some degree. I mean we're talking about a movie that miscolors Frenzy and Rumble even with a $6 million budget, added an extra Cyclonus to one shot for no apparent reason ("His Armada"), and
forgets a Dinobot through the whole picture with the exception of two brief shots. I think ascribing a ton of carefully planned directorial intent to the film is probably overthinking it on both our parts. If we're honest, it's probably more likely that they just wanted to get this shit done, and could not have cared less about the aspect ratio as long as it gets out the door on time.