The Command Menu (used in KH1, KH2, Days, and KH3) represents the fighting styles to Keyblade wielders who had to train on their own like with Sora for KH1. In CoM, it's obvious about the different battle style because he had to use the card system to progress through the castle as he forgot about how to fight normally. By KH2, his memories were brought back by Namine and continued training himself like how he used to. In account for Roxas in Days, since he's Sora's nobody and was created during the events of KH1, Sora's abilities during then were practically carried over to him. In account for Coded (original), Data Sora was probably just programmed with only an attack command for use at all times. Don't know why, but, eh.
The Command Deck (used in BBS, Re:coded, and KH3D) on the other hand represents the fighting styles that Keyblade Masters use and wielders who are pupils under a master as seen with Terra, Ventus, and Aqua in BBS, and Sora and Riku in KH3D. For Re:coded, Data Sora was programmed from a Keyblade Master, Mickey in this case, and since he didn't travel with Sora during his adventures, Mickey probably thought he fought like a master, thus using the Command Deck.
For KH3, Sora returned to the Command Menu since in the end of KH3D, he went on a more personal journey and probably reverted back to the Command Menu as that's the fighting style he's used to and probably stuck with that for the rest of KH3.
I dunno. Just a thought. What do you guys think? Maybe add on to it or make up something better?