Well, I have mixed opinions on the subject.
To an extent you (the article writer) are absolutly correct about Champions Online and the style, but I also suspect that a lot of this comes from current pressure on the gaming industry over content like violence, sex, and gore. Champions Online has ultimatly become the anti-thesis of such things, and honestly I think it did that by intentionally staying away from things like playable super villains and a lot of the dark hero motif. Please note that I would like a lot more "realism" and "gritty" type comic stuff, but I understand why they didn't go in that direction.
It's also noteworthy that one of the problems MMORPGs in general suffer is the need to pack interactive content together. For example, in World Of Warcraft something like "Elwynn Forest" or "The Blasted Lands" would be huge, not something you can traverse in length in a couple of minutes. Not to mention the tens of thousands of people who would live in Stormwind. However the reality of game design, not to mention fun (ie not travelling through an empty world for an hour or three for the sake of a realistic portryal of how things would be) requires a bit of leeway.
I think it's an unfair criticism to point out that for example Snake Gulch is right next door to both an Atomic wasteland AND a terrorist base. No that isn't even remotly sensible, BUT by the same token it's no worse than how content is arranged in every other MMORPG to date. Sure seperating the Atomic Wasleland fromt he Amusement park by a substantial distance would make sense, but is it really gamable?
I do tend to think that with the depth of the liscence they chose too much silly to be honest. Though again I think they did that for a reason. Truthfully Foxbat (the guy with the foam sign fanboy bots, and the pingpong ball gun) who is a giant send-up on Batman is overused. He is however no worse than many similar humor-themed characters in existing comic universes which tend to be used in doses. Like say Marvel's "Arcade", "Madcap", or "Brother's Grim", or well... quite a few people in the DC universe especially in the Batman rogue's gallery (and allegedly he's Mr. serious story himself).
Now yeah, Snake Gulch is a bit much at times. What could have been a very interesting concept, inspired by the movie "Westworld", does get a bit out of hand. But still you find that villains like Mechanon seem to be fairly serious concepts, compared to say Foxbat or even the GI Joe inspired tech terrorists (Viper = Cobra, even some of the constumes are the same).
I do like my over the top super hero game though (lifetime subscriber), and yes it has used so many jokes that it has become a joke. I still find it entertaining though.
It is NOT what it could have been, but I blame the industry for that. I think this game is what it is specifically because of fear of groups like Australian Censors. As things stand now Champions Online is a good product, albeit one that was not intended to push any boundaries.