There are 3 main styles of crossover i see.

Singular Omniverse/ Worlds Collide - This is when the characters or elements of one series come into another series from their original universe and the two sides interact. Or perhaps the two serieses are in the same universe, just different planets or far away from each other? That falls here as well. Warhammer 40k: Courage and Honour and Friendship is an excellent example.

Meshed Time Line - Similar to Worlds Collide, except the defining feature of this subset is that the two worlds share some common element that's instrumental to the story. Pony Space is a great example of this. Equestria had it's own Black Marker and a necromorph incident prior to Isaac showing up. The entire driving force behind getting Isaac was to help with Equestria's problem. Rebirth of the Damned is also straddling this line. Hoennshy may fit this trope as well.

Alt Reality - When the crossover is directly integrated into the canon lore of the world the author creates until it is neither one nor the other. Fallout Equestria is the best example of this.

So my question to you is, which do you prefer and why?

Personally I prefer the Alt realities and Meshed Timeline stories more. The writers have to take that extra step in world building to make it all work, and the extra effort is easily seen. Not saying that Worlds Collide is bad, but there's just something about the world building in stories like Fallout Equestria: Heroes, Mane Effect, Tales from Mystika: A My Little Mages Book, and Deus Ex: Equine Revolution that tickle my fancy.

I really like the Meshed Timeline/Alternate Realities style.

Allows you to create a whole new world.

I'm not a big fan of crossovers but the ones I like are: a good part of the fallout equestria, sweetie's mansion and sweetie chronicles so I think my favourite type is alt reality

I'm more of a singular omniverse/ worlds collide kind of guy. I enjoy finding ways for the two different series to relate to one another, and its a lot of fun mixing them up and seeing how the characters react to one another.

I like to do meshed timelines. It's what I'm actually doing right now (A mesh of three universes into one big one)

It's a longshot, but I think I can relate Halo to Command and Conquer and MLP at the same time. (Kane is Forerunner, Scrin is Flood counter but went rogue, ponies genetically engineered but warped to save them etc.)

Singular Omniverse and Worlds Collide is my fave. Meshed timelines at a close second.

Alternate Reality: the idea that something like the LOTR timeline being canonical in the MLP universe interests me.

Thanks for the shoutout.

Obviously, I prefer Worlds Collide, because in my opinion, the entire point of a crossover is to see what happens when worlds collide. In my case, we see 40k Space Marines and Tyranids landing in Equestria; how much more drastically different could you possibly get?

In regards to Meshed Timeline, I do rather enjoy it, but the problem lies in the two worlds that are being meshed. It is a tad difficult to find parallels with MLP in a universe like 40k. Well, actually the Horus Heresy and Nightmare Moon were disturbingly similar.

Alternate Reality simply is not my cup of tea. Fallout: Equestria is an exception, but in my opinion, this genre of crossover is not so much world-building as it is shoehorning pieces of two worlds together. The end result is too often just ponies copy-pasted into another world with maybe a few alterations to really "ponify" it.

This reminds me: I really need to read Fallout: Equestria.

Omniverse and Alternate reality are my favorites.

I like Omniverse/ Worlds Collide, actually working on one. Basically, Tanith First and Only cross-over. I think that this type of cross-over gives the biggest amount of place to put awesome references to the original.

In my opinion, it depends on what's being crossed over, but generally, I like Worlds Collide, especially when you cross overr stuff like Kamen Rider Decade or Kingdom Hearts, where World-Jumping is already an integral part of the concept.

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Ditto. It depends a lot on what you're crossing with ponies.

My Little Destiny, for example, takes the ending of Stargate Universe -- the team is forced to go into stasis as the Destiny is too low on power to make a FTL jump to the next galaxy, so it will take lifetimes before another gate comes into range -- and wakes up the humans near Equestrian space. This puts the ponies both in the far future and distant location, but it also meshes extremely well with the ending of the series it's being crossed with.

My Little Denarians uses the concept of the Outer Gates of the Nevernver -- little is known about what lies beyond the Outer Gates, because the Seventh Law of Magic forbids even seeking information about what lies beyond them. In My Little Denarians, ALL of fiction lies beyond the Outer Gates, including My Little Pony. The Nickelheads end up hooking up with Discord, screwing around with Celestia, bonding demons to several of the Mane Six, and sending them to other fictional universes to pick up powers to bring back to Nicodemus. Fluttershy, for example, visits Skyrim, and picks up the powers of the Dragonborn. Harry also chases down some of the Nickelheads in Star Wars, and his magic manifests as Jedi powers while there. (Irony: Since The Dresden Files is fictional, it would also then be beyond the Outer Gates... )

Back to Equestria adds a gem and a switch to the DeLorean. The new switch lets the DeLorean travel to the MLP universe (where it can then travel through time).

The Rise of Iron Mare is Iron Man retold using MLP characters. It begins very similar to the existing Iron Man media, but soon takes a sharp turn, accomodating the personalities of the ponies rather than the humans they've replaced in the story.

Archives of the Friendquisition is a future Equestria, which has turned out similarly to the human empire in Warhammer 40,000.

My Little Exalt combines magic Twilight discovered in On a Cross and Arrow (unattributed) with the power of the Well of Udr in the Exalted roleplaying game -- the Well is, in theory, a single point of connection between all universes.

"Random portal sucks characters into alternate reality" is a pretty common crossover trope, and sometimes it can work. But mostly, the actual crossover event should be worked into the actual story/setting of at least one of the sides of the crossover. It makes suspension of disbelief so much easier. (Not a crossover, but Versus Equestria has Trixie attempt to pull a rabbit out of her hat, and she ends up pulling a human out instead. He's just as confused as she is. She names him Rabbit.)

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The worlds collide is interesting, but I find the Meshed Reality a lot more enjoyable. It just allows a more interesting narrative and allows you to create something new and original