I kind of get the feeling that this remake will actually end at the first boss fight against Jenova. That's a really good breaking point to stop, with the sequel starting up at Costa Del Sol. This also makes Condor Mountain a pretty good post-game spot that would be exclusive to this first game, and completing it or not affects future games, particularly in whether or not you get the Huge Materia.
The next game can be hyped up as featuring Dyne, Vincent, and Cid, and end at Temple of the Ancients. After the temple gets destroyed, the party fights with Sephiroth (which wasn't in the original) and after winning, Sephiroth controls Cloud and the game ends shortly after.
The third game opens with Cloud waking up in that village I forget the name of. From here on out, Aeirth is out of the party, just like from the original. This game includes Aeirth's death, Cloud falling into the lifestream, and his eventual recovery. The final boss will be Cloud's memory versus Sephiroth's memory in the lifestream, and the game ends with Cloud's motivational speech on the Highwind.
The fourth will be the final game, including Diamond Weapon, Proud Clod, Hojo, maybe some other shit I'm missing, and the general game's final dungeon and ending, as well as the rest of the Huge Materia quest. Ultima Weapon as an optional super boss, but they probably won't include Ruby and Emerald. Also, while there will certainly be an underwater mako reactor dungeon, I get the feeling that the submarine won't be a vehicle; it'll just be for cutscenes, basically.
I want the Wutai sidequest to be in the game, although I'm not entirely sure how they'll implement it. I think it would be best to make it mandatory and give the story a reason to have to go there, which would also mean making Yuffie mandatory at some point too. Not entirely sure how I feel about that, but it's not too bad. This is what, I feel, would be pretty ideal for it being episodic, but I doubt we'll get this.