The TV series and the comic books must take place in different universes. That's really the only logical way to explain all the differences between them. What differences? Well, now, I'll list all the ones we've been able to find so far.
1) The comic books have a more serious feel to them. The stories are more
dramatic. Some are genuinely moving. The characters' personalities are thus
somewhat different. They're more serious in the comics than on the show.
2) Mega Man and Simon Belmont aren't in the comics. Rather, Samus Aran from the game Metroid is there. Samus was never on the TV series. There's no explanation given for this difference.
3) Uranos, one of Mother Brain's minions in the comic books, isn't on the TV series.
4) Kid Icarus' toga is white on the show. It's yellow in the comics.
5) Lana's outfit is pink on the show and purple in the comics.
6) They never mention the word "Nintendo" on the TV series, but they do in the comic books.
7) Kevin is called "the hottest Nintendo Power Player on the face of the Earth" in "WELCOME TO VIDEOLAND", something most definitely not supported by evidence on the show! Kevin was losing to King Hippo while playing Punch-Out in "KEVIN IN VIDEOLAND", and in "NIGHTMARE ON MOTHER BRAIN'S STREET", Kevin says to himself: "What would you do if you were sitting in front of your TV now playing 'Wizards and Warriors'? Oh, you'd probably lose!"
8) The biggest difference is in Kevin's arrival in Videoland. In the episode "KEVIN IN VIDEOLAND", Kevin is brought to Videoland by the Ultimate Warp Zone. He and Duke are shown as real-life characters for the 17 seconds it shows him in his room. In the comic book story "WELCOME TO VIDEOLAND", they're shown as cartoon characters in Northridge. True, it is a comic book, but it wouldn't be so hard to take scenes from the show and place them in the comic books. On the show, Kevin is using his NES Advantage. In the comic book, he's using a standard NES controller. On the show, his TV set (a Sony) and Nintendo control deck are on a stand. In the comic book, his TV set and Nintendo control deck are on a dresser. On the show, Kevin's sitting on a director-style chair. In the comic book, he's sitting in a (rather comfortable-looking) black chair. On the show, Lana, Mega Man, Kid Icarus, and Simon Belmont are waiting by the Ultimate Warp Zone for Kevin to arrive. In the comic book, only Lana and Kid Icarus are there, and Lana is holding her power scepter, a weapon which she doesn't even have on the show!
So what does all this mean? The TV series and comic books occur in alternate
universes! Think of it as watching the original 'Highlander' movie, and then
watching 'Highlander 2: The Quickening' (commonly known as 'The Sickening'!).
Same characters, but the two can't go together in any logical way. The same
is true for Captain N.