>>3834424
I think they probably needed to beef-up Barrett and Red XIII's character arcs.

In Part 1, they acknowledge the existence of Deep Ground, which was supposed to be a secret until Dirge of Cerberus. So they have Barret run through the tunnels under sector 7.
And they connected Yuffie's DLC and Part 2 sequence with Deepground, but if Dirge of Cerberus is to be canon then they can't go anywhere with it.

It's hard to say where they'll go in Part 3, because their character arcs have pretty much been exhausted. Barrett and Red hate Shinra, but not so much Sephiroth.

The biggest hole to fill is Cid Highwind. They cut "Rocket Town" from Part 2 and never really mentioned the space program.
Rufus is out there looking for "the promised land", but Palmer insists there's lots of Mako in space...and he's not exactly wrong.