I really would have liked to have seen a scene of Gerald/Shadow/Maria together, aside from them running away from GUN together. I didn't really buy Gerald's "break-up" with his Grandson, especially after they spent most of the movie acting like BFFs. The "You're no Maria" line really didn't feel earned, as unlike Shadow, we never got to see what he was like prior to her death. I think it would have also made Shadow seem less like a Yes-Man to Gerald in following his orders.
Was slightly bummed that they threw in "Live and Learn" but only did it in snipits in-between the comedic fight between Eggman/Gerald. It was still epic and felt earned, but the dramatic shift in tone every couple seconds felt like they couldn't effort to use the full song or something. I thought I heard a small snipit of "Escape from the City" when they jumped out of the helicopter. I don't recall hearing Eggman's SA2 Theme though.
The Super Sonic/Super Shadow fight was short, but easily the closest we might ever get to a proper live-action Dragon Ball Z fight on the big screen. lol
After Sonic gave one of his quill's to Eggman in the Trailer, I really thought they were going to have Eggman use Sonic's quill to power up a Metal Sonic reveal; but no, he "died" and there was an army of Metal Sonics.
I assume that they'll turn Metal Overlord into his own character independent of Eggman so the series can go on without/take a break from Jim Carrey, and have Amy Rose serve a similar role to Tails in the second movie to warn Sonic of a new threat. I assume Sonic Heroes will be the main inspriation, but I could also see elements of Sonic 06* being included if they wanted to throw in time travel/multiverse elements as a way to recast Eggman.
EDIT: I forgot that Sonic CD also had time travel. So maybe the Time Stones could be used instead, with the Metal Sonic army serving as Terminator stand-ins.