So in my fiction (a Crossover, adventure) the main guy Artix, a paladin from another world with a good heart that always helps those in need, is very energetic, but hate undead creatures as they killed his family and village but also when he slays undead it relishes there Spirit Orbs(souls) from the undead body. ( http://aqworldswiki.com/w/Artix ) (note: he is a pony while in Equestria)

He meets fluttershy…

Would making them in a romance be a good idea? Or would it seem unbelievable? Also im open to ideas to how to make it work

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Tragic past — check.
Overpowered — check.
Overly good — check.
Girls (Fluttershy) like him — Will you check this one as well?

I'm not pointing out that you're making a Gary Stue, I am pointing out, however, that you mentioned most points that describe a Gary Stue. If you're good enough author you can still make it work despite all that.

2622557 wow...in retrospect he kinda is i may have to change some stuff because i don't want a sue anything in a story