An option to select a so called "search mode" for the jogwheel, which increases the size of the steps when turning the jogwheel, as scratching through the song just doesn't work that well (I'm not a mouse guy

). (I'm using a RDJ2: IE)
Also the support of the 8 rotary ("clicks") buttons of the RDJ2:IE in FutureDecks Pro would be really nice, as they are useless in the current version
The support of mapping LED's on the controllers would also be an improvement

Also the
High Freq Filter on both decks (high as in HI/MID/LO), doesn't seem to have much effect on the actual sound.
The mid freq filter cuts to many freq's.
Also I had this weird glitch: the faders seemed to be leaking sound when they were at 0. Didn't reoccur though.
A feature in FutureDecks Pro that automaticaly detects whether a song is playing, or not, and shows this by highlighting the play button.
-edit-
I like to see an autostop feature at the end of a track, as the track still plays even if the track ended.
-2nd edit-
Pitch Bend feature for the RDJ2:IE (by default pitch bend mode is on when you start FDPRO, then you can select scratch or search mode)