The movies are based in part on the Ultimate line of comics,where Nick is indeed black and done purposely on Jackson's likeness ot the the point where they had to let him play the role in the movies to use it.
Correct - there's been an African-American Nick Fury that looks like Samuel L Jackson for over a decade.
http://en.wikipedia.org/wiki/Ultimate_Nick_Fury
It is not odd for them to use the Ultimate Fury here. Most of the Marvel Cinematic Universe takes at least some influence from the Ultimate line. The "Chitauri" from the Avengers movie, for example, are the Ultimates line version of the Skrull...