Some my own ideas, others suggested by various anons.
 
1.Anon is injured when brought, hurled, taken, or falls into Equestria, when found he is taken to a hospital upon treating him the doctors confuse his appendix for an organ that all Equestrian natives use to generate magic, not aware that humans lack magic they assume his was damaged in transit to Equestria and hastily transplant a minotaur's in hopes that it will suffice. Through the wonders of "its magic I ain't gotta explain shit" it works, Anon now has magic, though how it affects him will be up to the writers imagination.
 
2.Anon has been living peacefully in Ponyville for 3-4 years, when he discovers that Twilight had discovered a way to send him home only a year after he arrived. Furious he goes to the other 5, only to discover that they knew already. They had in fact decided as a group that Anon was better off with them. Angered beyond words he heads too Celestia for help dealing with the mane six who are trying convince him to stay. Only for Celestia to admit she knew as well, and joining in on trying to convince Anon to say.
 
3.When Anonymous goes to sleep, he finds himself in Equestria. When he wakes up, he simply disappears from there.
 
4.Anonymous finally went full horsefucker and is dating a mare (author's pick). The problems arise when Anon's special somep0ny starts to hint at courting another mare (under the fanon that ponies are polygamous) he refuses, only for his mare friend to introduce him to numerous mares in hopes he will change his mind.
 
5.Magic is naturally drawn to living creatures, many Equestrian natives evolved to utilize magic, Anon not being native his body simply "ejects" the absorb magic with an empathic effect dependent on his emotional state. (this could be used to explain why ponies would be drawn to him)
 
6.Anon is being haunted by the ghost of Starswirl the Bearded, who only Anon can see and hear.
 
7.Anon is a bear disguised as a human.
 
8.Ponies really like having Anon ride them like horses.
 
9.Celestia reveals to the public that her and Luna's father was a human and that human + mare = alicorn, much to a non-horsefucker Anon's chagrin.
 
10.Anon joins the mane six in a expedition to a distant jungle, while traversing it they come across a tribe of humanoid primates who believe Anon to be a prophesied hero come to save them from a monster who demands yearly sacrifice.
 
11.Anon is a violent hillbilly who constantly tries to convince the denizens of Ponyville to chase away/lynch Zecora.
 
12.Anon literally has more penises than he knows what to do with.
 
13.When vising a restaurant catering to carnivores Pinkie REALLY wants a trucker hat that can only be won by eating a 10 pound steak, Anon being the swell guy he is, takes on this challenge.
 
14.Anon is a slightly unhinged inventor who finds a way to use atmospheric magic to power his machines. Antics ensue with his inventions.
 
15.Anon's is a giant robot and fucks Celestia's castle.
 
16.Ignorant of Equestria's reversed gender roles Anon constantly acts in a way that leads the denizens of Ponyville to believe he is a floozie, despite not have even been in a relationship since arriving in Equestria.
 
17.The reason Equestria doesn't have many non ponies living there isn't because of bigotry, but because ponies consider intelligent non ponies exotic and desirable, but most other creatures consider ponies unappealing.