Some guidelines that a Sonic film might follow to provide a consistent thematic timbre.
1: The Theme of Versus
Sonic's story to my mind is composed, intentionally or not, out of two part conflicts of interest. Interestingly these contentions are parallels to each other and with a little tooling all feel fully associated and complimentary.
-The Mobians versus the Humans.
This should really be the central conflict even, more then the battle between Sonic and Robotnik, which really mirrors this conflict as well. The mobians and humans each have true grievances with each other, back stories defined by their choices and beliefs rather then some sort of simplified distinction of good and evil purely because of race. It's not only a racial contest but also one between factions of what each represents
-Nature versus Industry
Sonic has from the get go had a subtle context surrounding the juxtaposition of emotionless metal machines and vibrant but fragile natural creatures.
The SATAM show distorted this nuance with a popular theme of environmentalism.
Although this remains a trendy message for filmmaking today I'd shy away from making the conflict as overt as an appeal to green politics not because of the sensitivity of the subject but because political themes can override every other idea very easily and become the focus. To keep the themes universal and timeless there should be a more general impression of the battle between living and manufactured, animal and man, nature and civilization. Both have their vices and virtues. For instance nature and animal can be savage, man and machine orderly and respectable. In the end the conflict should be a talking point, a subject of investigation and not a platform for an opinionated implication.
-Sonic versus Robotnik
According to the official Sega Sonic storyline as well as the Western animated series and comic book lines, Sonic shares a surprising number of similarities with his nemesis Robotnik. Both are social outcasts (and in some versions, both orphans) with great intelligence and skill that came into use following unforeseen events. They both rose to the occasion and became great figures but on opposite sides. Considering that Sonic's speed and coloration came from an experiment that Robotnik performed, Sonic literally owes a lot of himself to Robotnik: quite literally in many ways one of his creations. This metaphor extends to the fact that Sonic wouldn't be a rebel leader if it hadn't been for Robotnik's invasion. Sonic and Robotnik are both revolutionaries in their own right and both driven to their actions by the subjugation and enslavement of their people. Sonic is very nearly Robotnik in so many ways that he's constantly in danger of crossing the line and letting anger drive him to becoming his foe.
In this way the fight is on two fronts for him: external and internal.
-Sonic versus Sally
This is more of a playful rather then an earnest contest but no less heated. Sally represents the upper class (being a princess) while Sonic is decidedly low born despite his father being a famous soldier since his legal guardian, Uncle Chuck, chose to live in working class exile. Sally is also a thinker where Sonic is primarily a doer without thinking and she prefers meticulous planning to Sonic's reckless gambits.
But they're enough alike that their attraction isn't unwarranted. Both enjoy adventure. Both are firm defenders of the natural over the mechanical and their friends against any enemy no matter how numerous of powerful. Both have a mischievous streak and a brush of sarcasm, which translates into quips, joshes, and taunts. They're also physically attracted, but repulsed by the very idea of attraction which makes their relationship one that is in continual flux but also evolution. A good writer could manage to keep Sonic and Sally's attitudes towards each other advancing and deepening even as it wavers or drives them into contention. The main reason I like this particular couple in fiction is because they were never quite in love just because Sonic was the hero and she the heroine. There's plenty of other woman and men vying for both of their attentions: yet another divisive but interesting factor to their ongoing feud.
2: Story Addition Suggestions
These are some bonus side plots that might help to make Sonic a deeper cinematic production.
-Can't Go Home Again
Sonic and friends are the rare example of nomad heroes. In the show Knothole forest was practically a vacation resort because of it's childhood demographic presumably, but the comics made it much more plain that the Freedom Fighters are constantly in a war zone without terra firma. If Robotnik could muster the resources it would be the work of a moment to wipe his enemies away in a surgical strike. Famous the Archie comics had Robotnik in a single war machine nearly beat Sonic to death and dismantle the rebel base completely, forcing the Freedom Fighters to flee.
So why not take that to its logical conclusion?
Superman belongs despite his displacement because he has an alter ego and home city. Spiderman's identity as Peter Parker has a loving aunt and a job.
Oddly the most kindred comic character Sonic has is The Hulk. Both characters are pursued every day of their lives and they can't cast off their fugitive status because it's based on who they are. The Freedom Fighters are without country, without home. Even the camp is a temporary shelter not a permanent base: a place to hide not to settle.
Imagine what you could do with this unique circumstance?
The Freedom Fighters in addition to cobbling together living quarters could try and recreate their society, but as they remembered it. Perhaps the kids could convene for a national anthem at a set time just to recall what it was like to have a nationality.
With more emphasis on this alienation even something as innocuous as Sonic's recurrent love of chilidogs takes on a new dimension. It's not only his favorite food; it's a reminder when there was abundance and a recollection of happier childhood days.
I think the stakes and what the Freedom Fighters stood to gain could be graphically illustrated by the rebels clinging to what few remnants of their lost city Mobotropolis they had. People caring about things can instill the same interest in an audience if it rings true. To make the cause of the rebels significant they should consider it as such. Words carry less weight alone then if a material 'totem' supports them oftentimes, and with this running theme there could be considerable gravity applied to an otherwise cursory situation in the past. The fight for the rebels isn't just against Robotnik, it's for a new stable sanctuary, a better livelihood, and a return of all that was taken from them.
-The Freedom Fighters versus The Imperials
In a classic sense the rebellion in science fiction and fantasy is fighting for a complete reinstitution of the original power structure. The Hobbits are going to destroy the ring of power so they can restore what was, and the Rebel Alliance in Star Wars is fighting to re-establish the Old Republic. It could be presumed that the Knot Hole insurgency is trying to bring back the original kingship since Sally Acorn is a surviving royal.
But what if this wasn't the case?
The original Acorn dynasty may not have been a utopia. Sally is a tomboy, which may imply she felt suppressed by her surroundings when she was princess (yes, in my version I'd call her queen). She might not be keen to go back to a life in which she wasn't entirely free to make her own choices and do things that woman and royals aren't supposed to. Sonic may actually want to return the imperia more then Sally because although his experience has always been the under class, he's strikes me as the sort who would be a good patriot on principal. This would create a sense of tension between many of the Freedom Fighters who would otherwise be allies; not even a violent tension so much as an ongoing ideological disagreement.
Should the Freedom Fighters even reinstall a kingship at all if they win? This question would loom large as survival gave way to battle and battle at times seemed closer to victory then ever before. What kind of decisions do you make when you're truly the only remnant of your society? Rebuild, or build over again perhaps better
There may even be other scattered colonies of the Acorn administration that persisted with the fall of Mobotropolis and, when they discover the existence of the Freedom Fighters in Knot Hole, maybe they may provide assistance or withhold it if the rebels are fighting in either the cause of a new society or the old. This kind of suggestion that this particular rebel coalition is not entirely united would imply individual thought on the members and factions within the cause: much more depth then we've ever seen in a Sonic story before but depth I believe it can support.
The title is Sonic the Hedgehog, but it's as much about his world as it is about his personal story. One part of that world, going by the idea that Mobius is Earth in the future, is the original dominant species now emerged from hiding underground: the human race. Sonic comics (probably in an unsophisticated bid to trumpet the horrors of environmental degradation) tended at least at first to portray the humans as near cavemen like berserkers called Overlanders, or ignore them entirely. Later additions to the story added the human population centers of Station Square and Central City, but basically reconstructed a prosperous, modern western/eastern civilization in both without much explanation why.
I like the idea of taking both concepts but making them a little more realistic.
Human survivors on the surface (what few they were) may be near feral and mutated, but not ravenous monsters without thought: more like early tribal societies. Those lucky enough to get into an underground bunker city have much more access to technology long forgotten in the over-world, but ironically find themselves behind mobian technology because the bunker civilization is essentially a slightly futuristic version of our own frozen in time: the old war machines of the twenty third or so century still in working order but only just. These humans are the ones with the resources to establish cities like Station Square but instead of being cosmopolitan recreations of New York and Tokyo I'd imagine them more like cities in construction behind massive guarded walls.
There are nomads too: humans looking to stake their claims in the rejuvenated world where the forests have invaded the mainland and once mighty municipalities have becomes arboreal ruins. Imagine Mad Max meets Firefly: hardy but suspicious settlers of a hostile wilderness with an invested interest in caring for their own.
The humans could provide a whole new feature to the Sonic mythos. Not only the mobian's story would be told but a whole other race with their own customs, equipment, and attitudes. Their race is opposed to the mobians thanks to a long-standing blood feud, but with the rise of Robotnik's global agenda perhaps more then a few of them will decide that past quarrels aren't worth being evenly split during a war which threatens every living thing.
Sonic's game adventures have always featured him leaping and darting along massive roadways and loop-de-loops, in between narrow walls, and amidst an obstacle course of gun toting robots. To translate this into a sci-fi interpretation of the story would be remarkably easy. Ruined freeways twisted by earthquakes become ramps and circuits. Jutting rebar can serve as handholds and grinding rails. Ledges of gutted high-rises can be climbed or run along. Imagine being an ultra fast, agile, reckless youth with an entire world designed by fate to be your gymnasium. You'd almost relish the opportunity, despite having to flee for your life every day. Freedom has its cost, but its perks as well and the action of Sonic nimbly turning the wreckage of the world into an expression of his independence would be a visual metaphor of his inner thoughts; the same thoughts he's reluctant to share aloud.
Certainly the future is a grim one, but it's also as you make of it, which could be a running idea of the film as a whole.