Out of all the dates and all the cut-scenes in the game, Yuffie's the only character who actually kissed Cloud, even if it was just a coy peck on the cheek. That counts in her favour somewhat. Her date with Cloud was quite adorkable.

Also, the fact that she's 16 isn't technically an issue in most of the world, although someone of that age dating a 21-year-old would generally be frowned upon. Exceptions apply, of course - see Lorde and her boyfriend for a real-world example.

Cloud has all the emotion maturity of a teenager, though, so he and Yuffie are probably a better match than he would be with Barret.