i want to animate this scene with falling leaves using the particle system but they are not transparent for some reason. (you can still see the wireframe and on a darker background it seems to be black where it should be transparent) but why?!
Those are Freestyle outlines. If you don't want them you can turn Freestyle off in the Render tab of the Properties panel. Or, if you want them but you don't want them on those particular meshes, you can add a Material stroke modifier under the Properties panel->Render Layers tab->Freestyle Line Style->Alpha. Then set the Freestyle stroke alpha to zero in the leaf material. Or, you can model the leaf shape more accurately and stop using alpha on that material entirely. This would help a lot with the problems you're having with the mist, too, and I would personally recommend that you model the silhouette of the leaf a little more meticulously to help with that.