I'd prefer a mix of the two systems myself. A couple of years back, I would probably have been all over the idea of the command deck system, but after playing through the Final Mix versions of II and Birth by Sleep consecutively, I can definitely see some of the issues from the latter.
For me, the classic system can be the core. The combat for the most part should be similar to Kingdom Hearts I and Critical Mode in II where you have to be strategically ballsy if you want to win. Tech points definitely need to be a thing again (really missed those in the later games). However, there should also be a system where Sora can customize some moves and create either a couple of standard attacks or Limit Breaks. This is where the command deck system can come in and be strong. Just combine a couple of spells/actions for a new attack/Limit that isn't too overpowered and I think it can work. Just don't link movement abilities such as High Jump or Arial Dodge or Glide to them. I also don't want to see actual abilities like Second Chance, Once More, Combat Boost, etc. to be tied to these, either. I love breaking Birth by Sleep, but I don't think that would be optimal for Kingdom Hearts III; give us a hard, yet fair challenge. Make abilities something that Sora gains naturally through leveling up or story progression.
I mentioned that I don't want movement abilities like High Jump and Glide to be tied to the command deck. Ironically, however, I wouldn't mind being able to create a couple of abilities that can be used for movement despite being meant for combat. Be honest, how hilariously awesome was it to go to Pete's Rec Room as Ventus, go outside and use two/three well used and leveled up Sliding Dashes in order to reach an area that you are meant to use Glide so that you can get Superglide early? I wouldn't mind using some of these abilities to think outside the box for certain things like that. I know that's partially more of a level design issue, but I thought I just throw that out there.
I've noticed that I have been all over the place on this subject, but another thing that I'd like to say is that the magic system NEEDS to be based more on Kingdom Hearts I. As other have mentioned, the magic system in Kingdom Hearts II was simultaneously too easy and too cumbersome. In the first game, you had to play skillfully in order to gain more magic through hitting enemies or being hit while having MP Hastega equipped. I know some are going to mention MP Gift, but even there, you won't always have that if Goofy dies or doesn't have enough MP, especially in Final Mix where it was somewhat nerfed.