My favourite boss in tales of series Barbatos Goetia from Tales of Destiny 2. Even if I fought only the first, he was very interesting! The fight was really intense, and his mecanisms of fighting are so clever, so good to add some difficulty to a newcomer player! And on top of that, of course, the voice of Barbatos Goetia, is so well done. Norio Wakamoto's voice fits well with Basbatos' character. He plays cruel characters so well, he truly is a bad guy seiyuu!
Kratos, EX Dungeon, Vesperia Loved him in Symphonia. Even if he is/isn't the same person in Vesperia, it's worth every bit of time you take to fight him and get to him. He was always one of my favorite badasses, so when I saw him again in this game I was like HELL YEAH.
I've only played Xillia and Vesperia, so my opinion on the boss is entirely based on those two games. But I really like the final boss of Tales of Xillia because of how crazy the scenario is and how they get to that moment. I don't want to spoil it because the story of that game is pretty nice, and if you haven't played it you should definitely fix that.
Oh wow, I didn't know you could fight him in Vesperia. I really need to get all the way through that game - I've only seen a fraction of it so far. My favourite, speaking of which, is probably Kratos from Symphonia. Any of his boss fights, really, though the final one (before you can potentially recruit him) is pretty awesome. It has a personal stake that a lot of the other fights in the game lack.