Oh yeah, don't get me wrong, jokes here and there aren't bad. Take a Sonic story and remove the humor altogether and you get Sonic 06, which of course is not gonna fly with anyone, even the serious story people.
There needs to be a balance. Sonic can be light-hearted, but he also needs to realize that what's going on is no game. Sonic Colors and every game past that has Sonic acting like saving the world is like an office job, just something he does because he has to and it's nothing more than an irritant. He never takes the situation seriously.
Lost World TRIED to make it somewhat serious, but all the plot points felt unearned and a lot of stuff went absolutely nowhere. The Deadly 6 just exist, there's no reason for it or motivation for why they do what they do, no backstory, nothing. They're colorful stereotypes. Why are we beating them up? Because it's a video game and they're the bosses. Oh, okay.
All I ask is for them to give us a reason to care. If Sonic doesn't care, then why should we? Story makes a bigger difference than anyone might expect.