Well, on the subject of whether it was sex or not, first, I completely agree with fishsama. They specifically got a special director for that scene. If it was meaningless and Cloud rejects her off screen, why all the trouble?
And what he said, they used a classic movie style to imply intimacy.
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Nomura spoke in reference to a
defining moment near the end of FF7. During an intimate moment, Tifa tells Cloud that "feelings aren't conveyed by words alone." Players are lead to their own
conclusions, as they watch Cloud and Tifa wake up together the next morning.
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II. The time Cloud knew Aeris, he was part Cloud, part Zax. Therefore, it is possible that the part of him that was supposedly attracted to Aeris could have been Zack. Remember, he finds himself during disc 2, after Aeris dies.
Well, he doesn't really show that much interest in Aeris... or Tifa during the first disc, unless you let him. There's a quote somewhere that says he's oblivious of both girls.
However, if you reverse what you said, that Aeris' feelings are because of Zack, well... here's what SE has said.
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Aerith's feelings for Zack explain why she acts the way she does around Cloud in FFVII.