"Unique" means "having no like or equal", but it can also mean "limited in occurrence to a given class, situation, or area" and "unusual". To be "unique" doesn't always mean you have to be "one-of-a-kind", like Mewtwo is.
Every region has their own unique Legendary that other regions don't. Doesn't mean that Legendary can't travel on their own to a different region. They are unique in ways that differentiate them from regular Pokémon. When you put it in that context, there isn't a single Legendary that isn't unique. You can say the same with all kinds of Pokémon: they're all unique in their own way.
And who's to say a Legendary can only have one of each at a time? Some, like Manaphy and Ho-oh (I'm sure), are justified. However, there are hints that go to show Legendaries are breedable, they just don't breed in the games. Remember the baby Lugia? The mother wasn't the same Lugia from the Orange Islands (most likely, though I like to joke that the Orange Islands Lugia fathered the baby, hurr hurr). And like the above poster said: Latios and Latias live in small herds. And in the fifth movie, we do clearly see a father Latios with his two children flying to Altomare. People may speculate they're just hallucinations of the movie Latias and her brother as younglings, but I really, really doubt it. And then there's the Darkrai Tobias has. Is that the same Darkrai from the movie? Highly unlikely. Some of these Pokémon we just don't really have the answers for.
There's also the whole "a" and "the" issue, or just a lack of the two. In the anime, characters have said "a insert-Legendary-here", hinting that there is more than one. If you say "the", or the two words are absent, then we can safely assume the Legendary in question is one-of-a-kind.
So, you're asking for something that hasn't yet existed, for all Legendaries are unique. Unless someone can come forward with evidence to show there's a Legendary that has the qualities of a common Rattata, then there's nothing to compare.