What was the primary difference between presidential and congressional reconstruction plans?

The main difference is the 10% rule, the Presidential Reconstruction accepted it and the Congressional reconstruction rejected it.

Explanation:

The Presidential reconstruction started with Lincoln and eventually ended with Johnson and the presidential reconstruction applied the 10% rule that determined that the state could re-enter the union when 10% of its voters took an oath of allegiance and pledged to abide by emancipation.

The Congressional Reconstruction started when the Johnson reconstruction ended and rejected the 10%, instead it imposed a radical reconstruction, which imposed harsh standards on the Southern States such as the Wade-Davis Bill.

he supported the seperation of church and state. he also promoted religious tolerance.