My guess is that the ending with Fitz was because the actor may or may not have committed to coming back for a second season. I know the actor has a movie coming out so it's possible that either him or the show runners decided he needed a break.
We got to see Fury reveal his blind eye. In the comics of course he was portrayed as wearing an eye patch
but in The Avengers he did not have one. With Captain America: The Winter Soldier he is attacked and presumed dead, which set up the second half of the first season of Agents of SHIELD
, and from those injuries it looks like he'll be getting an eye patch in the movie universe now.
EDIT: Correction, Fury did have a patch in the movies. Not sure what I was thinking but at the time of this post I had a clear image in my head of Jackson as Fury without the eye patch.
Speaking of Fury, I wonder what role he'll be playing in The Avengers 3 and other movies coming out since he turned SHIELD over to Coulson? Does this mean a bigger role for Coulson in the movies or a smaller role for SHIELD in general?