I was thinking that instead you would be forced to walk through a forest area to get to Junon, and as soon as you enter you would automatically encounter Yuffie in battle. You will not be able to escape, and after the battle she manages to persuade AVALANCHE to take her along with the secret intention of stealing their materia at the right time. Visiting Wutai after Cid joins would also be essential to the story.
As for Vincent, I like Mr. Darkside's idea that obtaining him in the Shinra Mansion would be essential to continue. Perhaps a key to the library could be in Vincent's possession (I'm not forgettng that he was asleep for thirty years, but perhaps someone awoke him and gave him the key to the library before he went back to sleep. This would take place after Sephiroth burned down Nibelheim of course, and perhaps one of Hojo's 'acting' villagers could give him the key. It wouldn't be a problem as Sephiroth could walk through walls at this point).
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