There's nothing special about Loghain except that he does come with his own set of armor. You would be able to change it though. Since you get him so late in the game, all of his talents and skills are chosen already. So if you have Alistair built just the way you want him, it would be best to keep him.

The only reason to choose Loghain over Alistair is for story purposes. There are new things about the world that you can learn from him and recruiting him has some pretty big consequences in terms of plot. But, for gameplay purposes it's best to keep Alistair because he's already customized to your liking.