This is especially annoying for the RS/ORAS and XY.
RS/ORAS: Even if you didn't know about the other Legendary, it seems odd there just so happens to be another team who have their own theme which is opposite of that of the main villains. It almost feels like they themselves should be after a Legendary Pokemon of their theme. Not only that, we have the Red Orb and Blue Orb with one of them in the story being used to Primal Revert the mascot Legendary you gotta wonder what about the other one. It just feels there's a half missing (not helped in the remakes when the Granite Cave mural is split in half to only feature the mascot Legendary).
XY: While nothing really hints of their being another Legendary, it's more Lysandre's plan seems make a leap in logic. Lysandre's plan is to make Team Flare immortal and kill everyone else, two things which Xerneas and Yveltal clearly represent half of. Yet Lysandre only catches one of them but is still able to do both. Now I can come up with some excuses why, but to me the plan was clearly created with both Legendaries in mind so it feels like the plan is missing part of its power source.
On a slightly lesser note, though BW includes both Legendaries they do swaps something which to me doesn't feel right one way around. Depending what version to pick, N and the player character get assigned with being a hero of "Truths" and hero of "Ideals". To me it makes sense for N to be "Ideals" since he's the one trying to change the world to what he thinks is right meanwhile the player is "Truths" as you're suppose to represent that Team Plasma's philosophy is flawed. But if you got White version than N is "Truths" and the payer is "Ideals"... which makes no sense. If N is "Truths" then wouldn't that mean his and Team Plasma's philosophy is right and its the "Ideals" player protecting a false perception of the world? Worse yet, they're always giving or relating Reshiram (the dragon of "Turths") to N in other media like the manga, anime, and merchandise.