How much trouble you had with Emerald and Ruby should have no bearing on this; they're fighting each other, not the characters. Besides, if you have any idea what you're doing at all, they're both really easy.

Ruby would win this matchup, and it wouldn't really be close. However, it would take it a while to wear down Emerald's HP. Nevertheless, that would happen long before Emerald even got close to finishing Ruby.

Ruby has extremely, extremely high Defense and Magic Defense. Knights of the Round and Bahamut ZERO are often mentioned in strategies, because their damage totals are unaffected by the defense. I suspect that this what it means when the Bahamut attacks are described as "unblockable"; they cannot be reduced by defensive measures, similar to Pandora's Box.

However, Emerald does not have access to these abilities. Emerald has Emerald Shoot, Emerald Beam, (physical attack), Revenge Stamp, (eye HP attack), (eye MP attack), and Aire Tam Storm. Since Aire Tam Storm is based on materia, it would do 0 damage, as opposed to the 9999 most people see. None of these abilities would take off even 500 HP at a time on Ruby. Emerald's defenses are rather unremarkable; you can expect Ruby's attacks to be undiminished. This creates an enormous advantage for Ruby.

Now, Emerald cannot be removed by Whirlsand. I won't go into how ridiculous that notion is, but it's ultimately irrelevant, since Ruby will still win.

The only thing that could give Emerald a shot would be its "eyes" conveying it an enormous advantage in comparison with Ruby's arms. This is not the case, however. Ruby would still be able to attack from both sides, and Emerald's eyes would have no more luck against Ruby's defense than the main Weapon.

So, in conclusion to this unnecessarily long post, Ruby will always win what would always be a protracted battle.