I always thought that Kyon's (over) complimenting of Mikuru was more to do with the fact that he can't admit to himself that he actually likes Haruhi more. A kind of "No! Mikuru is the one I like, not anyone else!" type of thing
Almost 'forcing' himself to compliment her so he doesn't have to think of Haruhi.
That's just the way I saw it. ^^;