1: More Lupe. Also, bring back that wolf girl from No Brainer and give her a name and a proper roll in the show.
2: Flesh out some of the characters more, and have some episodes where it's the other characters who get Sonic out of a mess now and then. In general show that while Sonic's the big hero, that the rest of the Freedom Fighters are also valuable. This would also mean giving some names and personalities to the various unnamed Freedom Fighters we see in SatAM. So, that should satisfy the need some people have for introducing more characters, without resorting to characters such as Rogue and Shadow.
3: Tone down the annoyance factors of Ant and Dulcy without wrecking their characters.
3a: I kinda like how Ant would sometimes bumble into a solution, rather than finding said solution on purpose. Perhaps play that up to offset his cowardice. So, keep Ant as a sniveling coward, but give him an unusual amount of good luck.
3b: And for Dulcy: Not have her have so many head impacts. Failed landings can be fun, but not have every one end with her saying something about her "ma". And probly phase those out and have her learn to land properly. It seems to me that it's the constant "ma" references and head trauma that most people have a problem with in regards to her.
4: Tone Sonic down a bit. His attitude is a bit up into the 20 range. Dial it back down to 11. Still overkill and fun, but not 90s overkill. In general, not make us wonder why he even has friends in the first place.
5: Bring back the Sally-Bot. Perhaps with conflicting programming, due to the trip through the Roboticizer combined with Rotor's manual reprogramming. That could make for at least another interesting episode.
6: Avoid bringing in other game characters. Too much messing around with the SatAM formula would ruin it.
7: Minimize cultural references. The more you reference something that is popular now, the less someone 20 years from now will likely enjoy the show. In general, plan for the show to be popular for generations, and try to make it as timeless as possible.