I just finished rewatching Gurren Lagann and noticed there's quite a few similarities between the final bosses of Pokémon Super Mystery Dungeon and Gurren Lagann. It should go without saying there's major spoilers for both in this post.
The Boss
Hive mind of many different entities (bad thoughts and emotions in PSMD, the people of the Anti-Spiral home-world in Gurren Lagann)
Speaks in an all-present voice to lower the hero's morale (when I first played PSMD, I imagined Dark Matter's voice as the Anti-Spiral's for some reason)
Seeks to annihilate all life on Earth
Earth lost to the boss many generations before to the story (in PSMD they kinda defeated Dark Matter, but failed since it would be a problem again)
Until just a few days before the final battle, is unknown to the majority of characters in the story
Has the power to "permanently" immobilize people in another dimension that's actually possible to escape from (the Voidlands in PSMD, "extra-dimensional space, trapped in a series of universes that are created instant to instant as they are perceived" in Gurren Lagann)
The Battle
Reached after an almost non-stop series of smaller battles (starting when going to Revelation Mountain the second time in PSMD, started when departing Earth in Gurren Lagann)
Sacrifices are made to get the heroes to the final battle (they're less permanent in PSMD though)
Takes place in another, space-themed dimension (whatever it is in PSMD and "a super-spiral universe where thought is given form" in Gurren Lagann)
At least one hero was present in the first battle generations ago (Mew and possibly you in PSMD, Lord Genome in Gurren Lagann)
A former enemy is present to help (Nuzleaf, Yveltal, and the Beheeyem in PSMD, Viral in Gurren Lagann)
The heroes fight with a bigger, more powerful form (evolved forms and Tengen Toppa Gurren Lagann)
The finishing blow was dealt with the form available from the start (unevolved forms and Lagann)
Different themes play during the first and last parts of the battle, the first of which gives the impression of how serious it is and how impossible it should be, the second of which gives the impression of hope and how certain the heroes' success is
Everyone on Earth is able to watch and cheer the heroes on (despite most if not all Pokémon having been turned to stone in PSMD)
Upon being defeated, the boss talks about keeping the world safe in the future, which is agreed to (the potential for Dark Matter to return averted by Mew in PSMD, Simone agreeing to keep the universe safe from the spiral nemesis in Gurren Lagann)
The End
Getting a wireless call from a friend almost immediately after the battle, reporting about how everyone's OK (from Dedenne and Rossiu)
Returning home
The partner/Neia disappear after hanging on a little longer than originally intended
Emotions are experienced
The hero returns to his passion (expeditions in PSMD, digging tunnels in Gurren Lagann)
Credits, then an epilogue