Thing is I could actually see
these three separate plot lines intersect in certain intervals as while Kairi and Riku might be the ones primarily searching for Sora, both Roxas and Ventus are tightly connected with Sora and since they owe their new chance at life to him they might want to help out on occasion if their own plots allow it.
Naminé herself could be important to all three plot lines due to her memory-related powers although it could seem that she might fit in most with Ven's third her unique relation to Sora might involve her in Kairi's and Riku's third while her relation with Roxas and Xion might have her play a secondary support role in Lea's and Isa's third.
In general I think that a character shouldn't be too easily dismissed just because their current arc is done. Crafting and opening a new arc is easily possible.
Maybe they should even mix up the formula a little as in
Kairi actually travels together with Aqua and learns from her in the field while Terra plays main support for Ventus in his quest. Riku may switch at his leisure between either group or sticks with one of them while Mickey travels with the other.
Which would mean either Kairi/Aqua/Riku and Ventus/Terra/Mickey or Kairi/Aqua/Mickey and Ventus/Terra/Riku. The latter combination would also allow Riku to spend more time with Terra while Kairi would have the chance to truly develop bonds and relationships outside her already established trio.
Lea and Isa would obviously have Roxas and Xion as support, that wouldn't change.
Naminé I can see being somewhat of a "mission control officer" for all three groups, possibly relaying info from and to Yen Sid.