Take what I'm about to say with a shaker full of salt, because this is hearsay of hearsay. I have tried to find the original source of this information in the past and now, and I can't.
I once saw someone say (maybe here on KHI? I can't remember) that JP staff listens in on KH voice recording sessions; however, they don't have the level of English language expertise needed to direct voice actors (because even for native speakers, you need to know a LOT about language in order to make recordings sound convincing). As a result, they are largely working by ear, off of the rhythm and tone of the performances. This approach results in the stiff and/or awkward deliveries we hear in the final game.
This is just my opinion, but I think the original characters suffered the most from the voice direction (DEAR GOD, Vanitas, WHAT DID THEY DO TO YOUR VOICE). For the most part, the Disney characters didn't have it too bad, even if they were a little wobbly at times. It could be that Disney was maybe really heavy-handed with the voice direction for KH3, the way they were for other aspects of the game? That wouldn't explain why, of all characters, MICKEY MOUSE was a mess, but then again I never thought Bret Iwan bought into the role enough to make his performances feel authentic. He literally sounds fine in all other media as Mickey, it's just KH where he falters for me.... But I digress.
On a note that isn't pure conjecture, one confirmed reason for those awkward pauses characters sometimes take in between lines is because of the length of the Japanese lines compared to the English ones. Main installments may get re-animated lip movements, but the scenes themselves don't change. As a result, the timing is always better suited to the Japanese lines, and in instances where the English line is noticeably/significantly shorter (ie, in KH3D, the "All for one, and one for all" scene) we get the awkward pauses.