Pokemon Gold referred to Ho-Oh and Pokemon Silver referred to Lugia, but you could catch Ho-Oh after the E4 in Silver and you could catch Lugia after the E4 in Gold. I don't see why it couldn't happen with X and Y this time around. There's more than enough opportunity for them to have other legendaries that are version exclusives.

And none of the titles had direct sequels since Gen 2 (GSC technically a direct sequel to RGBY), until Gen 5 had BW2. And none of them had nothing but new pokemon until after the E4 since Gen 1 until Black/White. And every new pair was followed by a third version in every generation until the 5th. The "rules" of Pokemon games can change. There's no particular reason to assume anything specific about these games beyond the stuff we can get direct confirmation of (such as "six pokemon at once", for instance), or the stuff that is pretty much the definition of a main Pokemon game (8 main gyms, an Elite Four, etc). Anything which has changed once can change again.

But it seems like there's way too much reference in the titles to these pokemon themselves.  Gold and Silver don't exclusively represent their respective pokemon as much as X and Y seem to do.

Those names are pretty difficult to pronounce. I'll go with Legendary 1 and Legendary 2 this time around.

EDIT: So far I'm getting Pokemon X...

definitely getting X

loving this. can't wait to play.

I'll get 3DS and definitely the X version of Pokémon later this year.

if only... if only...

It's the 1st thing I thought of when I saw him haha.

I'm leaning towards Y