Hi, Here is an Epic Crossover Story Suggestion Trilogy That I Highly Recommend for you to make....
Story:
Installment #1: MLP: FIM/X-Men: DOFP/The Wolverine: Original Timeline
Installment #2: MLP: EG/X-Men: Apocalypse/Logan: New Timeline
Installment #3: MLP: PP/Deadpool/Legion: Parallel Timeline
Videos Further Proving My Point on this:
Installment #1:

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Hi, Here is an Epic 9 Installment Crossover Story Suggestion That I Highly Recommend for you to make.....
Note: (Involves An MLP In-Universe Version of the Spider-Slayers From the 3 Part Ultimate Spider-Man Vs. the Sinister Six Episode Spider-Slayers)
Story:
My little Pony: The Harmony-Slayer Saga:
Prequel Trilogy (The Harmony Slayer Origins Trilogy) (Takes Place in The MLP: FIM Pony World during the Time of the Aftermath of the 2-Part Season 6 Finale To Where and Back Again):

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http://www.fimfiction.net/manage_user/messages/9966068
Revolves around an Epic MLP Next Gen Crossover Story Suggestion that I Highly Recommend for you to make...Nuff Said.
with thanks,
From Your Biggest #1 Fan of all time in the history of all of existence,
Shane Nokes aka James Plasma aka Dark-Pulse/Darkimus

Here are the 2 Last Separate Crossover Story Suggestions that I Highly Recommend for you to make Which Follow the same Single Property Pattern as Power Ponyes: Dino Thunder and the 5 Other Stories I Mentioned Previously...
Story:
Standalone Story #1: Plague Inc./MLP: Multiple Epidemics in Equestria (a Crossover with the Famous Epidemic Based Simulator Game Plague Inc.)

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Hi, Here are 5 other Singular Property Crossover Story Suggestions That I Highly Recommend for you to make and just like the first one both focus on a single property and are all standalone Stories like Power Ponyes: Dino Thunder and are therefore more easily done....
Stories:
Standalone Story #1: Star Wars/MLP: Heavens and Stars (Crossover with The Star Wars Franchise)
Standalone Story #2: Ponynator: Genisys (Crossover with the Latest Film in the Terminator Franchise Terminator; Genisys)

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Hi, Here is an Epic Crossover Story Suggestion I Highly Recommend for you to make and this time is indeed based around a Single Property...
Story: Power Ponyes: Dino Thunder
Premise: An MLP In-Universe Version of the 2004 Power Rangers TV Series Dino Thunder...
Videos Further Explaining My Point on this:

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Hi, Here is are 3 Epic Crossover Trilogy Story Suggestions that I Highly Recommend for you to make....
Story Trilogy:
1.1. Halo: Shield-World-Celes-VII (A MLP/Halo Crossover Taking Place During The Post-Covenant-War Conflicts in The Halo Universe Version of the Milky Way Galaxy) (Takes Place In-Between Halo 3 and Halo 4)

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Prepare for the Apocalypse Wars...NOW!!!...
http://www.fimfiction.net/story/332409/equestria-girls-transformers-gi-joe-apocalypse-wars