I'm not sure if you know but just incase you dont...
When with wild double battles (riley, etc) you have to defeat one pokemon and then you can catch the other. Other than that a message will come up with something along the lines of , " There are too much targets maybe when there are less."
Personally I don't think that dialga and palkia will be in a double battle. For one they aren't so supposed to be best of friends in the first place. They wouldn't work together to fight one person, which sounds stupid. But then again games do have stupid stuff. Second, most people who play pokemon are 8 year olds. Nintendo is aware of how stupid people are. People are losing to Palkia and Dialga right now. (yes I know how stupid it is), Two mass legendaries would be a disaster for newbs. Unless they make the pokemon Level 30-40 instead of 47 then it might make the double battle with palkia/dialga easier.
I hope that they don't make Dialga/Palkia in a double battle. But it would make it an excuse for people to buy Diamond/Pearl. Since most people are too stupid enough to read the little manuals and don't know how to restart the game.
In all honesty, I know I'd love to have the chance of fighting two legends at the same time when I was 8. Specially when I have to choose one of them to _try_ to catch (as I'd only have one Master Ball, which would be thrown only at Giratina). But, considering Giratina will be at lv.47, theirs might be a little lower. I believe it's gonna be 40. Just because it's a round number (I know, 47...).
And about the friend thing, in the last japanese video people posted, both Dialga and Palkia are standing against Giratina. I know it's not a scene that'll be in the game in 3D and all that shit, but I think they'll still follow the "the enemy of my enemy is my friend" logic. While they weren't BFF in the 10th movie, the Rebellion pokémon has been summoned in the human world. And it knows OUTRAGE! It must be stopped, by all means.