In the midst of the battle venus would come in and try to stop them, this would distract Velen and essentially in the future bring him back to our side.
Then he loses control as Lucio attacks him once again. Then later on, the an attack by Velen would almost hit Nova but Lucio's brotherly love will kick in and he take control for a second and go in the way of the attack leaving Lucio fainted. Then Feathers or Nova can try to stop Velen before he goes on to attack Lilycove.
Hmmm, I really do like your idea Yanmega. And while it would be difficult to defeat Velen, there are a few things which could give us the advantage. One, as both Nova and Feathers have wings, they should have a speed advantage over Velen, allowing them to dodge his attacks while attacking from afar. And Dr. Grey is there too, with his Pokemon. That would mean it would be... what, nine onto one? With two of them being gods? I honestly think that would just tip it in our favor.
And of course, Lucio has dealt some damage against Velen, so yeah. And if all else fails, Feathers and/or Nova could switch into Beast Form. In other words, I think it's very much possible.
And as for finding the plates and gems, I think they should be in places or past guardians that can only be defeated by the Hidden One of the plate/gem's type. (eg. Feathers is in the sky, where you need abnormal flying abilities to survive in, Mensa's is past a psychically-responsive wall and Silver's requires a password in the language of rock).
Well, the Splash Plate was originally going to be in Manaphy's underwater city, where only powerful water types could reach, but due to a bit of a fight Manaphy and the People of Water once got into ages ago, it's ended up in that forest. The Flame Plate will probably be in one of the Volcano's, not quite sure yet.
Oh, and on a completely random note: Pokemon Abilities. What would your Hidden Ones ability be? Well, for Nova, her ability would have to be something exclusive to her when she doesn't have wings. Probably a fire type version of Volt Absorb - Flame Absorb. When she has wings, her ability would be levitate. Kane's would be Multiscale, just to give him a bit more of a reason to explain why he survived his battle with Kyorge, Manaphy and a whole bunch of Phiones.