Release check means that tapping a button counts as two presses. Think of it this way. Pressing the button counts as an input and then releasing a button counts as an input. That means with Kitana if you do a front punch then quickly do the down forward motion the fan toss will come out because it's remembering you releasing the button from the punch. This is called negative edge and it's common in 2D fighting games. MK typically has a very large window for this and canceling special moves from normals is common so a lot of serious players like to turn it off. If you're getting special moves on accident while doing normal moves consider turning it off.
Alternate controls basically turns all special move inputs into Street Fighter style rolling motions. So instead of doing down, forward+front punch for Kitana's fan you have to actually roll from down, down/forward, forward+front punch. Turn this on if you don't like MK style tap inputs.
Input shortcuts turns off any leniency on inputs. For example, by default an input of down/forward counts as both down and forward. You can do Kitana's Fan Toss with down forward, to forward+front punch. Turning this off makes the commands more strict. A lot of players want this to prevent accidental inputs.