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.
To me, the major difference between the two men's presidencies is that FDR was so much more assertive and aggressive in his policies than Truman was. FDR is known for the New Deal and for leading the US through WWII. Truman is known for .... almost losing to Dewey and holding up that newspaper with the incorrect headline.
But to me, this is largely due to circumstance. FDR was president in times of two of the biggest crises in the history of the US. He had to act in bold aggressive ways. By the time Truman became president, the domestic problems were smaller (no Depression) but the foreign ones were way more complicated (Cold War, particularly).
With no huge crisis to defeat, Truman wasn't going to look as good. With a complicated Cold War (and the Korean War) Truman didn't have the united support of the country behind him, through no fault of his own.