This is another big reason why I feel like there's a chance that the first game would make sense to end at Midgar OR in Junon before sneaking onboard the boat. They feel like natural cut-off points where the party can wander around on their own time that doesn't feel as though it's breaking the experience of the game. Both of them also lend themselves to placing content between releases in ways that're enjoyable as well.
I figure that weapon / item / materia sidequests as well as misc enemies are a good way to tackle it. One of the bigger questions I have is how they'll handle character levels between each part. Will players who do everything feel OP at the start of the next part? On the same note, that'll also feel interesting based on whether or not we get Yuffie/Vincent in Part 1 since if not, they might feel odd diving in and having them already have, or lacking abilities compared to other characters. That also ties back in to whether or not they'll be reworked to join you earlier if the game only goes so far in Part 1, so that you'll get enough time to really pal around with the whole party in whichever configuration you want.
X
Square needs to embrace the fact that players like to set their own difficulty. The ONLY time I've ever seen them acknowledge it in an in-house game is that KHII FM has a 0 EXP option, to cater to low-level runs. They did of course have Bravely Default, but that was mostly third-party work using SE's assets.
The smartest, most pragmatic thing to do is put a level scale-back mechanic, so that you bring yourself down to any previous level, including a recommended default for whatever area you're in. Everything else is a matter of player choice, as to whether or not to use the more powerful materia or weapons.
They made a huge mistake with XIII, and need to learn from it. Level caps DO NOT WORK.