My Reaction to OP
Quote Originally Posted by ToriJ
Metallo. I'd have Lex be more of a behind the scenes villain in this.
I think it would be interesting to see the process through which Metallo is created to battle Superman. I think maybe he should just be a typical battle drone created by Luthorcorp, powered by Kryptonite, and he would then be programmed with a false biography, giving him not only the mandated directive of destroying superman, but a near-sympathetic all-consuming urge to cause him anguish.

2. Batman

Under the Red Hood and Mask of the Phantom. A villain where you don't know who the person under the hood is.
Phantasm... Phantom makes me think of the Opera or that guy in purple spandex. I think maybe the first Red Hood should be the first Red Hood: Joker. This would enable his establishment as a recurring villain if perhaps only in the form Al-ghul assumed in Dark Knight Rises (which was incredibly lame but would make a hell of a lot more sense for the Joker), imagine Bruce coming face to face with a situation where he is so greatly tempted to murder his enemy rather than leaving them for the police and having the Joker's voice inside his head laughing until you hear Bruce laughing just like him. Another possible choice is the Batwoman. Darker and edgier could make her a murderous version of Batman.

4. Aquaman

Black Manta.
I'm not fond of the other Aqua-villains, though that's mostly because I've never liked their designs. They've always looked ridiculously stupid. Black Manta as a villain, I, a jaded fan of Young Justice, would hope this would lead to the introduction of Kaldur'ahm, (and Garth and Tula) if perhaps just in mentioning.

5. The Green Lantern

I'd flip it. I'd have the movie be out in space with the Lantern Corps as it should have been with Sinestro as the main villain.
I've always like Nathan Fillion as the voice of Hal Jordon. I don't think he's too old to play him either. He may have to trim up a bit but it's not as if he'd have to do any strenuous stunts. GL isn't an acrobat, he flies.

6. Flash

I'd just have the villain be Gorilla Grodd and make it Rise of the Planet of the Apes with Flash running around punching talking gorillas in the face.
While they've rarely done Mirror Master correctly, I've always liked him when they have. I feel that of all of Flash's Rogues Gallery, Mirror Master is one of his greatest foes, followed by Reverse Flash/Zoom and perhaps Captain Cold (when he can aim).

Anyway, so I get that this is all about Phase 1 and that may be because it is more difficult to imagine how you would go about getting the project off the ground, but I want to mention the foes I would use for Phase 2.

For Superman, just like in Man of Steel, I would use Zod. I don't think I would use his army... just Zod. His plot would be to try to restore his fellow Kryptonians banished to the Phantom Zone. The reason I'd hold off on introducing the mighty Kryptonian army is because I'd want to use them as the enemy force the team would fight in the second JL. Another option would be to use Bizarro as another of Luthor's attempts to match and destroy Superman. As such, it would probably be a better choice to continue the theme of Luthor as Superman's enemy behind-the-scenes and I could still introduce Zod and his army as the enemy force of JL. Obviously, the third movie, I would love to see Luthor whip out his massive anti-Krypton suit and go head to head with the Man of Steel. Some may say the third movie should feature Darkseid, but I'd save him for the third installment of JL.

For Batman 2 and 3, Black Mask and Hush. Two more characters whose identities he doesn't inherently know, whose crimes he has to actively investigate, and who both have wanted a place in the cinematic universe for a long time. Also, they both hate Bruce Wayne.

Second and third Wonder Woman, Ares and... I don't know, I can't find another one I deem worthy. Maybe the first Wonder Woman movie could be the first Aquaman movie (a la the upcoming Batman/Superman). So Wonder Woman would first face off against Aquaman. Aquaman would later face off against Neptune or Ocean Master.

Green Lantern provides another, more epic opportunity for JL3. That being Blackest Night. As for GL 2 and 3, I would say Atrocitus and obviously Parallax.

As a villain for Flash in the second movie (if having gone the way of Mirror Master in the first), Gorilla Grodd, followed by Professor Zoom in the third.

Yeah, I skimped on providing some reasoning and plot and such but it's late here and I'm lazy.