One idea could be that Godzilla somehow ends up in Equestria. The ponies are initially terrified but then realize Godzilla is more interested in protecting the land from some new dark force that has emerged there. Maybe Godzilla's size and power are a mystery to the ponies at first, and Twilight Sparkle tries to study him to figure out how he got there.
How about a Godzilla crossover with the Avengers? Maybe in a world where the Avengers exist alongside the Kaiju. Godzilla could be seen as both a threat and an ally. Iron Man could try to study Godzilla's power source while Thor might see him as a kind of primordial force. Captain America would be the one trying to keep everyone in line and figure out how to co - exist with this giant monster.
One idea could be a Godzilla crossover with King Kong. They could start off as enemies but then have to team up to fight a common, greater threat like an alien invasion. This would bring in the classic monster -vs- monster dynamic at first and then shift to an alliance against a new foe.
A Godzilla and Evangelion crossover would be cool. Godzilla could be the ultimate Third Impact scenario that the Evangelion units have to face. It would be a battle of titanic proportions with the mechs trying to take down the giant lizard using their unique weapons and Godzilla's raw power overwhelming them at times.
One idea could be that Godzilla arrives in the RWBY world due to a strange rift in dimensions. The Huntsmen and Huntresses initially see Godzilla as a huge threat and try to fight it. But then they discover that Godzilla is actually there to fight a common enemy, like a new type of Grimm that is immune to normal attacks but vulnerable to Godzilla's atomic breath.
One idea could be that Godzilla Earth teams up with a group of humans who have developed advanced technology to fight off an alien invasion. The humans initially fear Godzilla but soon realize they need his power.
One idea could be that Godzilla is drawn to the energy source of one of the Avengers' tech, like Stark's Arc Reactor. This causes chaos as Godzilla approaches the city where the Avengers are based. The Avengers initially see Godzilla as a threat and try to fight it. But then they realize that an even bigger alien force is using Godzilla's presence as a distraction. So, they have to find a way to communicate with Godzilla and work together to defeat the common enemy.
A possible plot could involve a dark force threatening both the world of Lucario and Equestria. A group of ponies and Lucario have to come together. The ponies use their magic and the Lucario use their combat skills and aura powers to fight off the common enemy. This would show how different abilities can be combined in a crossover story.
One idea could be that Thomas the Tank Engine somehow ends up in Equestria. Maybe there's a magical portal that transports him there. He could then interact with the ponies, perhaps helping them with some big construction project like building a new bridge. The contrast between his mechanical world and the magical world of MLP would create a lot of comical and interesting situations.
One idea could be Naruto characters suddenly finding themselves in the colorful world of MLP. For example, Naruto with his determination might inspire the ponies to face challenges bravely. He could teach them about the power of friendship in a different way, like how he values his bonds with Sasuke and Sakura. Another idea is a pony using Naruto - style jutsu. Picture a unicorn pony using chakra to perform a shadow clone jutsu to get more tasks done around Ponyville.
One idea could be that the ponies from MLP end up in the Underground world of Undertale. Maybe Twilight Sparkle could use her magic to interact with the magical elements in Undertale, like the SOULs. Another idea is to have Sans and Papyrus meet Fluttershy. Papyrus would be all excited to show off his 'coolness' while Fluttershy might be a bit shy at first but then they could become friends over their love for cooking (Papyrus loves making spaghetti).