The Boo you mentioned, or rather, the item that transformed Mario into a Boo in some games, would actually be a good idea - but more as an item than an assist trophy.
Captain N: The game Master: Using the pause button on his belt, freezing everybody on the screen for a couple seconds, except the one who called him.
Shantae: Either using her hair as a whip like in Pirate's curse, or one of her transformations.
Alex Kidd: Forces everyone (including the one who activated the Trophy) into a game of Jenken (Rock-Paper-Scissors). Whoever looses to Alex Kidd gets a Megaton punch from him, potentially costing a life.
Kammy Koopa: Blasting your ennemies with some spells for some time.
Baby Mario: Is in his bubble and crying annoyingly loudly, just like when you lost him in SMW2: Yoshi's Island. Everybody looses health or racks up some damage as long as he's crying.
The Nintendo eShop rating Thread: http://gamrconnect.vgchartz.com/thread.php?id=237454 List as Google Doc: https://docs.google.com/spreadsheets/d/1aW2hXQT1TheElVS7z-F3pP-7nbqdrDqWNTxl6JoJWBY/edit?usp=sharing
The Steam/GOG key gifting thread: https://gamrconnect.vgchartz.com/thread/242024/the-steamgog-key-gifting-thread/1/
Free Pc Games thread: https://gamrconnect.vgchartz.com/thread/248138/free-pc-games/1/