I'd love to write a Sonic the Hedgehog crossover on this site, I even have a basic idea for one but Sonic crossovers generally aren't well received...

My idea is pretty simple, a unicorn who's special talent is scrying magic, is asked to help out in an experiment with teleportation spells since she could track the object being teleported, the experiment goes horribly wrong due to a miscalculation and the resulting magical energies send the unicorn to the world of Sonic the Hedgehog, at around the time of Sonic Adventure 1 or 2.

Though said unicorn (I'm thinking of naming her either Scryer Gaze or Mirror Gaze) isn't a magical powerhouse her magical nature would register as something similar to chaos energy and could be picked up by scanners built to detect the chaos emeralds.

This is just an idea, I haven't really fleshed it out beyond that because I'm not sure if I want to write it or not.

6782461
It could work, but one piece of advice: one of the common downfalls of such crossovers is Sonic and Rainbow Dash. We know they're both fast, but using that as a basis for anything, be it a race, a partnership, a romance… whatever, will kill your fic. Either avoid the two ever meeting like the plague (such as Dash not having a role at all or using Sonic characters but excluding the Blue Blur himself), or be very careful to ensure that any interaction between them can't be simply summarized by the word "speed".
Also, another piece of advice: treating the Chaos Emeralds like a second set of Elements of Harmony will kill your fic. The Emeralds need to be used carefully, but preferably, leave them back on Mobius. No Super forms, no Chaos control, no Emeralds driving the plot, so you can be unique.
Another: Robotinik (officially, both names are right, so don't correct me) is used to death in the Sonic games already. Bringing him to Equestria without it seeming forced requires a delicate touch, like what Archie comics did when they crossed Mega Man and Sonic.
Yet another: Make sure neither side overshadows the other. You can have one side have the majority for a while, but eventually, the other franchise has to start pulling its weight and getting proper action, or they start to feel like filler.
There may be others, but these are the most common reasons those fics fail.
Hope this helps.

6782470
1. I have no plans to involve the mane 6, I just want it centered around the OC and her time on Mobius.

2. For the story, the Chaos Emeralds are ancient and very powerful artefacts- to the point where Eggman's or Tails' machines could only harness their power for a limited time before the machine just fries. Think of it like this- Pony Magic= Chaos Energy, Chaos Energy is a limited resource on Mobius because its difficult to collect and impossible to replicate 100% with their current tech, hence why Gerald Robotnik sought help from Black Doom when creating Shadow as the Black Arms had the tech to produce Chaos Energy. By that logic, Equestria is steeped in Chaos Energy so you can imagine what Eggman or Black Doom would do once they joined the dots.

3. Scryer has to go back to Equestria sooner or later. I was thinking of having Eggman learn about Equestria's magical properties and use Scryer as a power source to brute force a portal to Equestria, the Chaos Emeralds would be left behind, Sonic and friends hitched a ride and they would all be stranded in Equestria because Equestria's higher levels of magic would make it harder to force a way back. The local ponies would wonder what's going on and maybe the princesses would show up but by then the story would follow more slice-of-life stuff than action or adventure since Eggman's plans wouldn't really work out when Equestria's magical field fries his equipment.

I came up with this in like, ten minutes.

6782487
Found a problem: You said they're stranded. Traditional crossovers are supposed to have a point near the end or at the end where all parties return to their respective dimensions. You leave Sonic and pals in Equestria forever, you break the Sonic universe. You must allow them to go home at the end.

6782490
Good point, in that case the final story arc would be the characters working together to create a stable portal between both worlds, the Sonic cast could head home but have a way back to Equestria if I wanted to tackle the plotlines of other Sonic games or the other seasons of MLP, I know I want to use Sonic Unleashed and Black Knight in the future.

6782836
Stable bridges are an acceptable alternative. As are portals that may close, but some bad guy down the road may be able to tear open again. There are a lot of alternatives, but permanently moving prominent residents of one universe to another can have catastrophic consequences, whether simply their left behind friends and family thinking them dead, or even complete global chaos as order breaks down. Many fail to factor these in, but that just makes some fics some think are feel-good fics instead bring my mind to "offscreen horror".

Like how a certain someone who always tears prominent characters from their dimension at the end of their fics and plops them in Equestria has now set their sights on Star Fox, which means their ending will doom the Lylat system (Marcus McCloud, son of Fox, is supposed to form the third Star Fox Team with Falco as the Peppy (mentor) of the group to defend against a newer threat that isn't related to Andross at all, but is still dangerous enough to require a new team to assemble).

6782952
Most of my crossovers usually incorporate elements of both media for an AU with a defined end point, for example my Super Robot Monkey Team crossover features the Hyperforce stranded in Equestria but they will eventually leave at the end of the story because they are the sole protectors of Shuggazoom City. I prefer to use a mix of canon world building and my own ideas. My main worry is people simply not giving the story a chance because it will be a Sonic crossover.

Another example of my crossovers is Darksiders: Equestria's Tree of Life, Death and a pony are destroying the built up sources of Corruption in Equestria so Death can continue on his journey to save his brother.

I do my best to stick to what would fit with the thing I'm crossing MLP with and usually go for an Alternate Universe Equestria so I don't retread the same ground and to make introducing the non MLP stuff more interesting.

As in "Here's how this works in the context of the story". I try to make my crossovers interesting as "character from thing A meets MLP character B and stuff happens" doesn't really seem good enough for me when I have all this lore to work with.