Simon is something of a stealth Trickster Mentor that is trying to teach the rest of the team, especially Kevin, to be more functional. Simon seems to pull very sudden 180ºs from bumbling idiot to kicking serious butt.
Kevin is something of a sociopath that doesn't miss his home and zaps things to get attention (S2Ep9). Let's not get started on Kevin and Mike from the first season.
Angst? What Angst?: Kevin is in a world full of people he doesn't know, his sole companion from his old world is his dog, he's cut off from all that is familiar, and he's being forced into war. Possibly falls under Rule of Funny, as the only time he had the opportunity to go back he stayed because his mom told him to do his homework and take out the trash.
You either like Gameboy having his moments of snark and not being as clueless as the rest of the team, or you hate him for being a douche in his debut episode, which also had a large plothole regarding why Lana's father couldn't just come himself.
Simon Belmont is often decried for his whining, incompetence, snootyness and borderline-In-Name-Only appearance, but some fans looking back on the show find him more interesting than Kevin, as he was flawed and thus seemed more like a real person, plus he showed character development as the show went on, such as gradually warming up to Kevin season by season.
Reinhardt Schneider, one of the protagonists in Castlevania 64 and Castlevania: Legacy of Darkness, bears some resemblance to the Captain N version of Simon Belmont. Both have blond hair and wear blue coats with fuzzy collars.
Lana isn't based on any particular game character, but she still manages to bear a resemblence to one — Alis Landale from Phantasy Star I, a Sega game, who can even become queen at game's end.
And more recently, there's a playable heroine in Hyrule Warriors named Lana!
Simon's voice actor would later go on to play a prominent vampire character in the Underworld film series.
Donkey Kong is played by Gary Chalk. It wouldn't be the lasttime he'd play a famous gorilla.
Kevin and Mike have shades. For the whole show it seems like King Hippo and Eggplant Wizard are an old bickering couple with some slight abuse issues. This is kind of helped by the fact when they go undercover one is dressed as a woman.
Kevin and Link, in the Zelda crossover episodes.
I Am Not Shazam: Kid Icarus/Pit. One of the stronger indicators that the people working on the show had never played any of the games.
Narm Charm: This trope and the very premise of the show (kid gets warped into the world of video games and meets many NES characters) are arguably the only reason this show has the admittedly small following it does.
The Scrappy: Difficult to say, given the multiple bastardizations amongst the supporting cast. But even fans of the show generally hate Megaman and Kid Icarus due to their annoying verbal tics, Megaman moreso due to his grating voice and more blatant inaccuracy (even non-fans should be able to tell that Megaman should be blue).
Seasonal Rot: Among fans, the third and final season is the least regarded. Animation took a major step down and the running time was cut to eleven minutes so that it could be paired with Super Mario World. Additionally, everyone other than Kevin was used less often (in the case of Simon and Mega Man, it was most likely a result of Konami and Capcom, respectively, owning those characters and being entitled to royalties).
The episode "How's Bayou?" wasn't quite finished when it first aired, and as a result, several shots were missing their backgrounds. Reruns of the episode had the backgrounds intact, but for some reason, the DVD set uses the original, unfinished version, as does the version on Jaroo (the "Hulu for kids' shows" site).
The badly-drawn electrical current in the intro, which is followed by an Art Shift to ugly, monochrome CGI. Both of these were fixed in the Season 2 intro.
Stock Footage Failure: Early on in "The Big Game" Lana crashes into Simon and they land on the couch. The shot of the couch is copy-pasted from another episode, complete with the cast sitting on it, resulting in there being two Simons and two Lanas.
The episode "Mr. and Mrs. Mother Brain". Simon ends up under the influence of a love arrow and falls for Mother Brain. Alright, that's bad enough, but later on, Mother Brain ends up falling in love with him. Okay, really gross, but then they become engaged and almost married, and somewhere in between those two events Simon imagines them having children! Granted, this is all fixed by the end of the episode, but still! Gah!
It's only for about a few seconds, but in "A Nightmare on Mother Brain Street", Princess Lana was shown having Mother Brain's face! Doubles as Nightmare Fuel, even in-universe.
Suspiciously Similar Substitute: Mega Girl is quite blatantly meant to be Roll. Problem is, though, that Roll never received the same upgrades Rock did (outside the realms of fanfiction). In addition, Mega Girl is depicted as Mega Man's love interest, whereas Roll is Mega Man's sister (Classic Roll, at least, as other incarnations of Roll, namely Roll Caskett and Roll.EXE, have canonical romances with their respective Mega Man).
Kongoland and Donkey Kong are pushed in the opening credits of the first season as heavily as Kid Icarus, Castlevania, Mega Man and Metroid. All the other worlds listed produce major recurring characters, but Donkey Kong? Of course not. He shows up five times in the whole series and that's it.
With Punch-Out's King Hippo as one of the main villains you'd expect a Punch-Out episode or at least other characters from the game to appear. Nope! All you get is a one minute scene in one episode of King Hippo's world, featuring no other game characters and that's it!
More importantly, why couldn't Link have become a permanent member of the N-Team?
When you really get right down to it, this whole show is one big They Wasted a Perfectly Good Plot: A mega-crossover between videogames could have been brilliant if the writers actually bothered to research what games they were using.
Ugly Cute: For all its horror value, "Mr. and Mrs. Mother Brain" does give us the strangely adorable baby brains.
What an Idiot: Wishful Thinking has the N-Team coming across a magic lamp with a Genie that can grant any wish. And while Lana briefly considers it, no one uses any wishes to defeat Mother Brain or wish for King Charles to return.
The N-Team are gone for 3 weeks during their quest to find the Warp of Life in Happy Birthday Mega Man. Despite that absence, Mother Brain and her henchmen don't even attempt to conquer Videoland, nor does the N-Team acknowledge the possibility or even mentioning the villains at all.
Kevin completely forgetting about the pepper in Burger Time.