I think that almost any character in Sonichu could be interesting if enough thought is put into it. That being said, I did some thinking and I conjured up some alternate versions of our favorite heroes.
Chris - Instead of being blood-thirsty and bombastic, my version of Chris has him as a well-meaning but meek young man who never wanted to be the mayor. Having been thrust into the highest position of power in the land, Chris finds himself confused and deeply tired by his mayoral job, of which he scarcely understands and barely wants. He is deeply ineffectual at keeping the corruption in the government of CWCville at bay, but not out of malice. He often gives the impression of not being fully in charge in CWCville, as though he were taking his orders from a higher authority...
Sonichu - A headstrong young pokemon/hedgehog thing who presents himself as being cocksure but is secretly deeply insecure and anxious about life. He struggles to find his place in the world as one of the few of his kind. He feels dejected by both pokemon and hedgehogs as he is not truly either. Regardless, he maintains a certain upbeat quality even in a world where everyone is pessimistic. His optimism counters the pessimism and callousness of most of the other characters in Sonichu.
Magi-Chan - A stoical, deeply intelligent and introverted psychic. He is not particularly interested in socialization and subsequently resigns himself to work (IE, preventing crime) most of the time. He is well-read in philosophy, law and history, leading him to often question the dubious morality of his actions and assigned tasks. He detests Chris and the government he rules over but he keeps this to himself. He is profoundly lonely deep down, desirous of someone who will appreciate him.
Punchy and Wild- A pair of belligerent and frequently boisterous Sonichus who live to roughhouse. Punchy is a pugilist who is seen taking a great deal of joy in fighting (A la, the Orks from Warhammer 40K) and he is generally depicted as being somewhat thick-headed. Wild is a talented albeit lazy and hedonistic 'chu who would much prefer to just party and have fun then do any work. Neither chu takes any interest in politics or the motives of the government and the villains. The two are close friends and their antics frequently cause hilarity to unfold. They are still the comic-relief characters, so-to-say.
Angelica - A frumpy and soft-spoken Rosechu who maintains a facade of being a zealous, celibate and utterly devoted nun. In private, she experiences a great deal of cognitive dissonance between her accepted values and her intrinsic desires. She is a closeted lesbian, a fact that she desperately tries to suppress and eradicate from her being. She hates the dogma that she forces herself to swallow but cannot bring herself to admit her distaste for it. Her bottling up her emotions leads her to frequently be stressed out and on the brink of snapping at other people.
Blachu/Blake/Whatever his name is - A nihilistic counterpart to Sonichu who rejects the whims of society and defines his own morality. Like Sonichu, he goes to strenuous lengths to discover where he belongs in this world. He is frustrated by the excess and amorality of CWCville and is very cynical as a result. Additionally, he chooses to fight alongside the other villains on the side of evil as he is unimpressed by what passes for "good" in the world of Sonichu.
Mary Lee Walsh - A dissatisfied and deeply moral revolutionary leading a rebellion against the CWCville government. After a city-wide suppression of intellectuals and the educated, Mary raised her banner in protest, calling the people of CWCville to arms. She despises Chris and the corruption he presides over but she does not see him for what he truly is.
I would have put down something for Bubbles but I honestly couldn't think of anything.