No Export for You: Inverted? The last season only aired outside Japan, despite a full Japanese voice track being produced.
The Other Darrin: Unlike the games in 2003, the Anime featured different voice actors from the 4Kids line up such as Jason Griffith as Sonic and Shadow, Amy Palant as Tails, Dan Green as Knuckles, Lisa Ortiz as Amy, and Mike Pollock as Dr Eggman. They would later replace the game voices as the official voice cast until 2010, when all but Mike Pollock would be replaced with the current voice cast.
While not too different from the how the show actually turned out, there were a few elements that were definitely scrapped or changed from the second pilot.
Ryan Drummond was going to be the voice of Sonic in the dub, much like in the games until 2005. But then 4Kids said no.
From the same episode as E-90 Super Sweeper (aka Thunderbird 2), the launch sequence for the new X-Tornado (the collapsible palm trees) is also a shout-out to Thunderbird 2's launch sequence from the puppet series.
Mothra and MOGUERA appear in Episode 48 on a mysterious island. Mothra's a bit more vicious-looking and antagonistic (a nod to her dark twin Battra) and MOGUERA is based on his Showa appearance and battles Sonic, Knuckles and Rouge at the climax of the episode. Godzilla also appears as a statue that Bokkun sits on for a minute before it crumbles apart when MOGUERA appears.
Chris' attempt to use the Martial Arts moves he learned between season 2 and 3 (and falling flat on his butt because he's been grown down to the age he was in season 2) is a reference to Dragon Ball GT and how Goku had similar problems.
Might be stretching it a bit, but during Episode 60 Chris and Cosmo watch the last report from a damaged space colony, with the reporter◊ on screen suspiciously resembling Kimba.
One popular sub used the same font that was used for the subtitles in Sonic Adventure DX.