It's a matter of scale. Benchmarks are horrible at it.
There isn't really a whole lot of reasons for the Motion and S3 to score differently. Same processor. RAM isn't really a issue unless you tax the system. Same with the GPU. So you run into the matter of scale. The Motion has a little less power in the real world but less to run. The S3 has a bit more power but more to run. In the end they scale to being about equal on the benchmarks.
Benchmarks aren't really designed to compare things this way. They are designed to compare similar products. A Motion shouldn't compare benchmarks with a S3. It should compare benchmarks with other 3.5" phones. Just as the S3 shouldn't compare benchmarks with a Motion. It should compare benchmarks with other 4.5"+ phones.