I think of it like in Ratchet and Clank. Sure, its your average Save the Universe type plot, but the characters do more than just talk about how the Universe is in danger. They have their own little quirks that influence their dialouge, their histories are referenced heavily, and most importantly, interaction with circumstances and setting.
The best thing I can think of for this is with Tails. In Unleashed, he's been studying with Professor Pickle, and from my point of view, Pickle views Tails not as a student due to his age, but more like an intellectual equal, a colleague if you will. So I got the idea; what if, in a Direct sequel to Unleashed, Tails becomes an instructor at Spagonia university? I myself would find it humorous to see the 8 year old fox introduced to the story while teaching a bunch of human college graduates how to build a plane or something, talking to them like an ordinary college professor.
And references; in Unleashed, that reporter woman gives you a quiz in which you can answer saying that Tails is really a girl. While I don't think that misconception should be directly acknowledged in the story, I would like it if Sonic finds some sort of ray gun in Tails' Workshop, and, surprise surprise, it turns out to be a Sex-changing Transformation Ray. If that is the case, it is my personal opinion that someone must be zapped, and also that the gun must make return appearances throughout the story.
Or maybe that's just me.