That's a very large topic and I won't be able to do it justice in this space, but here are some comparison points to consider:
1) FDR was elected four times, while Truman was elected once. It is safe to say that FDR was much more popular, and that popularity lasted over time.
2) FDR had huge national crises to deal with: The Great Depression and World War II. In part, this is what made him a great President, that he was able to deal with both of them and bring us through it. Perhaps Truman would have been a better President if he had been the leader during those times.
3) Truman was the first President to deal with the Cold War, and he responded well. I believe FDR would have done as well, had he been healthy by that time.
4) FDR had a popular war, World War II, while Truman had a much less popular war, Korea. It made it harder for Truman to do much during his Presidency.