1) A crossover with Batman villain scarecrow- Jonathan crane was sent to live with Sunset shimmer due to the desicion of the court after his grandmother's death.

2) A story based on the clone wars- after the finale, Sombra returns with an army and new allies to dethrone Twilight. The first story is about one of the new allies- General Inogma, a beast that command Sombra's armies, capture Shining Armor, and it's about Flurry heart.

3) Wallflower summon a monster that connect to her emotion and kill those who brings her pain, anger, and other emotions.

3) MLP adaptation of Far from home with Luster dawn as Peter.

Which story should I do?

7036977
I like option three because it's something I would write, but that's what I like.

Have you tried instead of doing a crossover, taking elements of and writing a story that way?
Imagine option one this way:

Let's say a pony who's fascinated with emotions, mainly fear does dangerous experiments with it.
Something goes wrong and he becomes an avatar of Fear. Maybe he has to scare ponies to death so
he can stay alive and not be tortured? Maybe it's like a Dr. Jeykyll and Mr. Hyde situation, where he doesn't know at first he's the Avatar of Fear.
He has to find out over time what he does when he falls asleep.
The rest of the story is this pony's fight to against his darker impulses.

You can use as much as you want from the Scarecrow.
The story could be pure MLP without extra stuff.

7037214
That sounds interesting, but to me it's not what scarecrow is about, I would do it more about a scientist that kidnap ponies and use special potions to evoke fear.

7037270
Try it that way then.

When you use elements of, you don't have to do a crossover.
This gives you more freedom to do what you want and mix and match.

You could mix in other stuff from other mad scientist movies like, "The Fly" or "Splice."
Not quite sure this would work with what you're doing though.

You could mix in stuff from HPL's, "The Reanimator" if you wish.
You don't have to be faithful to DC's Scarecrow.

7037635
So here's the idea. Starlight Glimmer meet a pony in the library and the two talks about science, and Starlight takes him to ponyville. Meanwhile Twilight notice there are ponies missing. It all connected as the pony kidnap ponies to use his potion to create fears for study.

7037851
Sounds good.

7037856
I had an idea. A vampire pony hunter team up with the CMC to save the main six from Dracula. The vampire hunter is a raccoon that Dracula cast a spell to turn him into a weapon, but the raccoon ran away and found pair of guns. Sounds good?

7038854
Better.
Don't deprive yourself of the fun of making things up.

Or you could do this:

A pony vampire hunter has to team up with the CMC to stop an ancient alien vampire from unleashing doom on all of Equestria. A sentient racoon from another world is also after the alien too for revenge.

This version gives you more freedom.

You can use whatever you wish from whatever you like.
Wanna throw in some HPL refs for the alien vampire? Go for it!
Wanna use some guardians of the galaxy or sly fox, go for it!
Wanna throw in some Castlevania refs in, go for it!

This story will feel more yours because you will be mixing and matching elements.
It is more work though.