I agree with Cameron that it's best to rephrase the statement to "he is taller than his mother." However, of the two options you offered, "compared to his mother, he is tall" is better than "compared to his mother, he is taller." The implication might be that he is not particularly tall, but he is tall when compared to his mom (who must be fairly short.)

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1. Compartively speaking, he is taller than his mother. 2. Some students are happier in open classrooms than traditional classrooms.