I think the covers are there just to grab readers' attention. It's not like they're gonna break the forth wall or anything like that during the actual story - unlike the earlier semi-canon issues. Humor like that is now reserved for the "Off Panel" series, which has greatly improved since Ian's revival of the series.
As for a proper portrayal, everyone has different tastes. For me, if it's too lighthearted and cartoony, you get AoStH (which is rather annoying). If it's too dark and edgy, you get "Shadow the Hedgehog" and "Sonic 06" (which don't feel like Sonic games).
Personally, I think the comics have found a good middle-ground between lighthearted and serious. The lighthearted/humorous moments are used to heighten the series' whimsical atmosphere, while the more serious/darker moments are reserved for drama and character development.
I don't agree the comics have a found that good mix at all, but if you do, ok then...
I didn't like the Matrix so I hope not.
But LaserX has a point,
Flynn usually is the one to pull out forgotten characters and story elements and hold them as canon or important now (Larry Lynx, the Nerbs, so on so forth), that it seems almost careless to forget the Knuckles did die, prevented the destruction of his entire race, and lost his Father, then call this Knuckles's Most World Shattering event (unless of course they kill like Julie-Su or Kneecaps or his mom....).
Also, Personally I think the series HAD a good balance on comedy and serious, but has lost it. Perhaps things will fix themselves but I think the balance isn't perfect anymore. I feel too many issues are either too goofy and then the next too dark.
I'll be seriously ticked if Flynn dares to kill off or even hint of possibly killing off Julie-Su or his Mom for more nauseating shockvalue, especially with such a goofy cover. As if the comic cast hasn't been hammered enough...
It's no secret that this guy never has liked Knuckles' soul mate. He rarely even uses her in his stories, and this one she should be her biggest role yet with Mecha Sally in the picture.