Link is a good "all around character" and also very available to get. Zero Suit Samus isn't out yet and I'm assuming she will be hard to get like the others. As for choosing only ONE, that's a hard one. I main Ike and had to buy him from Japan due to his seemingly rising unicorn status. Marth and Shulk would also be really good due to their unicorn status.
I am kind of disappointed that you can only use them in smash vs and nothing else. If you could use them as a companion in the other mini games then they would be awesome. Right now though, I'm collecting more for the detail of the figures then playability of them, and Link is the only one I've actually registered in game haha.
TBH, I started off thinking "I'm only getting Link, Ike, Sonic and Megaman", but now I have about 10 and rising due to how cool they look on a shelf...
Edit: For a real recommendation I would get whoever you main. While you train your Amiibo they will learn from you, but as they get better you will also learn from them and in turn become a better player with your main.