@Jarkes  
I actually watched that on Youtube the other day, it was the second “Tetris” episode, I recall. It’s especially “dark” if you remember how bright, happy, and peaceful things were on the world of Tetris in the previous episode.  
It really shows the Puzzle Wizard turned their world into a “crapsack” world. Said Wizard even forced Kevin into playing a game of Tetris, and it’s possible the blocks the wizard made him use might of been people. (Though, they didn’t have faces, and not all blocks are sentient, or were the Tetris people.)
 
It’s kinda like how Robotnik would “roboticize” animals in the Sonic cartoon. (Also, by DiC.)
 
Speaking of which, as you said having Sonic (and a few other third-party characters) in would be nice, but as the case with Megaman & Simon, they’d have to get permission from the third-party company to use him, and such which might be a hassle.  
(In fact, they had to cut out all the third-party characters in the comic book version of “Captain N” that used to run. Though, they compensated by adding characters like Samus Aran to the N-team, complete with the classic reveal of Samus’s gender. I guess Kevin didn’t beat that game in under 5 hours. Hehe)  
Though, Sega was cool with “Wreck-it Ralph” using many of their characters, and such.

@Beau Skunky
 
The original Captain N cartoon had one episode that was pretty dark, where a wizard turned people into Tetris Blocks that were still fully aware. Just imagine what would happen to those people if the lines cleared…
 
But yeah, a darker Captain N-like story would be pretty cool. In fact, I wouldn’t be surprised if there haven’t been at least a few fanfics with the idea.
 
…Also, they could have a Sonic the Hedgehog story and make fun of the old rivalry Nintendo and Sega used to have.

@lasty  
Yeah, that could work. I wouldn’t say as “crazy/nightmare fuel-ish” as “Adventure Time,” (love that show BTW) but I’d say because Nintendo in general is very light-hearted, yet tends to have some serious/dark aspects hidden under the surface, (just look at some of Kirby’s villains) it could work having a similar style, but not exactly like A.T.  
I’d say a new “Captain N” series should be more light-hearted, but have some darker aspects hidden under the surface, and have it’s dark moments to kinda like “Adventure Time” does, as you said. Maybe have some sense of humor, and self-satire within it kinda like A.T. has to.  
Like I imagine they could have a joke about Pit’s name-confusion, and such.
 
As a huge Nintendo fan, I’d love to help work on a new “Captain N” series. It’d be fun to retool, redesign, and modernize, and with Nintendo’s history of games, there’s alot more to work with nowadays then back then. We could even have a new original villain instead of Mother Brain. (Or redesign her, and be a li’l more game-accurate.)  
Like we could have an episode where they go to the Lylat System to help Team Star Fox fight Andross, or another episode where they go to Hyrule, have the N-Team enter an “F-Zero” grand prix race in Mute City, or like you said have a “Super Smash Bros. fighting competition” episode to.
 
And one thing I always wanted “Captain N” to do, but never did was cross-over with Mario. (Which was, because there already was a Mario cartoon running at the same time, but it would’ve been nice if they crossed-over with it.)

@Beau Skunky  
I’d watch it just for the Smash Bros. episodes.  
The overall tone and darkness, I think, would work best sort of like how Adventure Time does it. In general, it’s a kinda weird comedy with action where needed and many episodes are just kind of “new place or idea, let’s do something fun with it”. But occasionally, the Lich happens. For this show, it’s usually kart races, flying with Team Star Fox, or everyone is paper-thin. Then there are darkly atmospheric, kinda spooky Metroid episodes. Sometimes Mario Sunshine, sometimes Luigi’s Mansion.

I love these Diamond & Dazzle comics, and this one looks especially promising. I also think it’s funny how she’s arguing over the “right” way to play a game.
 
@lasty  
That needs a new modernized reboot, I say.  
(Especially, now that people who actually play video games now work in the animation industry. So it’d be a li’l more accurate.) Maybe make it a li’l darker, but still with some campyness, and humor.
 
The modern-day Pit (Kid Icarus) would oddly fit in with a new modern N-Team, and maybe have Palutena occasionally show up to help, or call for the N-Team’s assistance in their home game world. (I like how she’s more like a “caring big sister” to Pit, then a “mother figure.” Keep that personality to.)

Looks like the game is going to make then work together.

This kinda reminds me of that one part of the Super Mario 3D World episode of Game Grumps.