I always thought and I have always thought are for all practical purposes the same. "I always thought you were beautiful." means "At all times in the past, I thought you were beautiful." "I have always thought you are beautiful." means "At all times in the past, as well as at this very instant in time, I thought of you as beautiful." While there is a slight difference, they mean essentially the same thing. If the speaker felt that you were no longer beautiful, they really should add to the "I always thought you were beautiful." sentence "but that has changed.". "I always think you are beautiful." is closer to the "I have always thought you were beautiful" sentence in that it indicates that at all points in time, past and present, what the speaker thinks (that you are beautiful).

I always thought is past tense. I have always thought is in perfect present tense.