These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Hilarious in Hindsight: In Episode 7, after reading Bowser's letter, Mario says (in relation to Bowser's mention of eating a goomba), "Imagine being in Bowser's digestive system!" Coincidentally, one and a half years after this episode was released (which was 2008), the game Mario & Luigi: Bowser's Inside Story was released (in 2009), in which the brothers spend most of the game traversing Bowser's body.
Ash and Brock (and when Ash left, it became Brock and Gary)
Hype Backlash: Season 5 to an extent. It left Richard really upset as he believed he had wrote the best season ever for the finale and having read the negative reviews really bought him down. It thankfully died down with episode 75 which fixed up most of the season's problems and delivered a truly great ending.
I Knew It: Wario being the second Chosen One was one of the main theories of the fans
Narm: The blood effects used in one of the later season 3 episodes may come off as a childishly gratuitous attempt at Darker and Edgier. The creators may have realized this, because for some reason future fight scenes lack this effect.
Then in the finale, it is revealed Mario was significantly weaker during that fight.