It may be easier than you think, anonymous. Unless your team would have any reason to lash out at your pichu or unless they show any hostility towards him, it’s likely they’ll accept him with open arms, especially if you establish the fact that he’s their latest teammate. Also, don’t forget to inform them that your pichu is shy and came from an abusive trainer, and tell them that as such, they should treat your pichu gently until he becomes more comfortable with them.
That said, the tricky part is figuring out how to keep your pichu calm. It may be best to introduce your team members one at a time to him so he doesn’t become overwhelmed. It would be best to introduce your pikachu to him first, as it is a member of the same evolutionary family and is thus the most familiar pokémon to him that you have. Wait until your pichu seems comfortable interacting with your pikachu, then follow with your sylveon (an affectionate mammalian pokémon and thus most likely to be gentle with him) and your gardevoir (an empath and thus a pokémon ready to adapt to his moods), in that order. Hold off on introducing your flygon until your pichu has grown accustomed to your other pokémon—and you, for that matter. Then introduce them to one another in a very comfortable environment stocked with food and toys that may put your pokémon at ease. It may be a good idea to let the pokémon your pichu trusts the most (out of pikachu, gardevoir, and sylveon) to help keep him calm and to assist in facilitating his interactions with your flygon.
In short, it’s likely that your team will accept your pichu; it’s just that you should introduce your pichu slowly and with plenty of patience to make sure he’s comfortable at all times.
Best of luck, anonymous!
The Pokédex According to Bill 