Mario seems to be more upset that Luigi died in Season 2, as it was a motive for him gathering his friends to kill Sonic, but in Season 6, he was only very mildly annoyed when Soniqua spits fire at Luigi.
Lucca doesn't seem upset when her Epoch is destroyed in the near-ending of Season 6, and lets Tails and his friends borrow the other time machines with no problem.
Author's Saving Throw: Season 5 and 7 are both this to their previous seasons. As they both focus on a more simplistic plot and emphazises the humor on character banter rather than the mean-spirited tone of the previous ones.
Catharsis Factor: Those who hated how Tails acted in Season 4 find it extremely satisfying that he's now the biggest Butt-Monkey of Season 5 and eventually losing all his riches in Season 6.
Continuity Lockout: Despite the short run time of each episode and overall emphasis on comedy, the series was surprisingly tight with its continuity. Each episode was a continuation of the previous one, to the point where missing so much as one episode will leave viewers confused regarding the current story.
Crosses the Line Twice: Much of the humor in this series falls under this. For example, Tails bullies Sonic constantly throughout Season 4, but he sends in a freaking bomb to him for no reason at all. It probably wouldn't be funny if it wasn't for Sonic's passive aggressive remark after getting blown up.
Sonic: That's Tails folks! (Iris Out, before immediately going back to an annoyed Sonic) Seriously, what a fucking asshole, now I gotta go to the hospital.
Link for his over-the-top Camp Gay personality, funny lines, and his constant messing with Tails (especially after watching Season 4).
Genius Bonus: More like "Nerd Bonus" but it still counts; Sonic went broke after Tails invested his money in Dreamcast stock. Dreamcast was SEGA's last home console and had a rather short lifespan (only lasting less than 3 years, when most consoles last 4 or more). No wonder Sonic ended up losing all his money afterwards.
One of the alternate timelines Sonic ends up creating when messing with the Epoch is one where his series has completely fallen into obscurity while Crash Bandicoot retained his insane popularity from the late 1990s into the present day and was considered one of the top gaming icons. This episode was released when Crash's series was at its lowest point and was in very real danger of becoming completely forgotten while Sonic's was trending upward due to some popular releases. Flash forward a couple years and Crash Bandicoot had an extremely successful revival which rocketed the series back to the top while Sonic's series was once again on the decline.
The Starcraft episode focuses on Zerg assimilating DNA, which is something that is known in the backstory. Come Starcraft II Heart Of The Swarm, where you get to see this DNA assimilation in action... although the Zerg have to kill to assimilate the DNA as Eggman didn't die.
The episode before the season 6 finale had someone comment that Jim in the form of Yoshi would eat baby Eggman and only to hatch him out again. Needless to say, that's exactly what happens in "This Can't Be Good".
The Duck Hunt Dog was shown to be an aggressive fighter and, after being placed under the ownership of Soniqua, began battling Pokémon. Come to the fourth Super Smash Bros. game, a crossover between numerous video game franchises including Pokemon, the Duck Hunt dog is revealed as a character.
Idiot Plot: Sonic and the gang probably would've saved themselves a LOT of trouble throughout the series if they weren't so completely inept with whatever tasks that they were told to handle. Justified in that they're all self-centered idiots.
It's Short, So It Sucks!: A common complaint about the series is how short the episodes are, as most of them range from 2-to-3 minutes. This actually got acknowledged somewhat by Sonic in The Stinger to one particular episode.
Sonic: Okay, I know this episode was short but I might die next week! Doesn't that mean anything to you guys?! Jerks!
Jerkass Woobie: Sonic. Sure, he's a self-centered dickweed but considering he tends to get screwed over quite a lot, it's not hard to feel bad for him after a while. Taken Up to Eleven in season 4, where Tails practically ruins Sonic's life by blowing up all his money and bullies him constantly. It's also said in the first episode that Tails knew Sonic would lose all his money in Dreamcast and gave him the stock tip in the first place.
Tails: Let's not get into all the details about who purposely screwed who out of all their money.
Jerks Are Worse Than Villains: The series features Mario as a mob boss, Kirby as an Ax-Crazy psychopath that loves murder, and Sonic as a Villain Protagonist. But Tails is the one who gets the most hate from fans for his actions in Season 4: throwing drinks at people's faces, pissing on Sonic, and just acting like a total douchebag. Even Sonic, who tried to blow up a movie theater with dozens of people inside just to kill Tails in the same season, isn't hated as much.
Seasonal Rot: Some have viewed Season 4 as this, with the Kafka Comedy being cranked Up to Eleven to the point that the antics Sonic gets into feel more depressing than they are funny. Most of this can be attributed to the change in personality for Tails, who takes absolute glee in making Sonic's life a living hell.
Take That, Scrappy!: Most of Season 5 is basically a huge one for Tails after his attitude in the previous season. The first episode has Sonic punching him several times, neither Peppy nor Slippy have heard of Cash Explosion, and when he assumes that he'll be taking charge of the Star Fox; Peppy outright says no and picks Sonic instead. The next episode takes it further by making Tails being attacked by a number of Facehuggers, ending with a Chestburster coming out of him. And later on in the Starcraft episode, they all leave him holding up a wall while the rest of the gang and a group of Eggman-mutated Zerg have a party.
They Changed It, Now It Sucks!: Not too many people were happy when the series was moved from Machinima to the Happy Hour Channel, which resulted in a slight decline in viewership.
They Wasted a Perfectly Good Character: Some people were a little disappointed that "Eggette", Eggman's daughter, was simply just a "Can't Unsee This" of Eggman and one of Luca's children grown up, although that particular timeline could have been written out after the reset button was pressed at the end of Season 6.
Ugly Cute: Soniqua is weird and grotesque looking, but you can't help but find her adorable somehow.
What an Idiot!: These moments happen quite a lot throughout the series, with Sonic, Eggman, and Thunderhead being the ones who make the most of them.