Alternate Control is a feature which changes the inputs for special moves into a more Street Fighter-oriented type. It is turned OFF by default. Moves that require inputs such as d, f + 1 by default, will change into d, df, f + 1 if you turn on this feature, making it more like the execution for a hadouken in a Street Fighter game. The most obvious difference comes from moves with control inputs like b, f + 3. Alternate Control changes the control scheme for these moves to b, db, d, df, f + 1, which makes the move register as a half-circle motion control, instead of a simple back-forward move.
Alternate Control Example
Shown in the video above, I started by performing the Joker's b, f + 3 using Alternate Control OFF. By changing Alternate Control into ON, the input for the move changed into
b, db, d, df, f + 3 - which is evident in the leftside control display. The change is also shown in the movelist menu if you access it.