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.
One of the most notable in the series is Squirtle being a Kamina Expy, considering that Squirtle predates Gurren Lagann by several years (and had Kamina's sunglasses first).
Darker and Edgier or Lighter and Softer: Depends on where you look at. On one hand, there's The End of the World as We Know It, which makes the situation graver than the original anime. On the other hand, there are lots of Funny Moments that lighten up the story; even the Bad Future doesn't seem to be a gloomy waiting time for Sir Aaron and Arceus (eg Legendary Pokemon Three Legged Race). It also helps that Ash is essentially revisiting his past and, with the benefit of hindsight and stronger Pokemon, averts/downplays some of the more unpleasant moments in the original anime.
Mary Sue: There is a general view of Jessie's Cubone as this.