I don't think any president has ever won a *second* term with a reduced popular vote and electoral vote %age from his first election (as you mention, FDR did that for his 3rd term, but not his 2nd). It's happened where they'll win with a reduced popular vote but increased electoral vote and vice versa, but whenever both go down, then the incumbent loses. So if both go down for Obama and he still wins, it would be a first.
I think Wilson did...
No, his popular vote %age went up from 1912 to 1916. Of course, there was the special circumstance of having such a strong 3rd party candidate in 1912, but it still doesn't quite meet the criteria being described here.