Start with a "World's Finest" movie, call it "JL: World's Finest"... Make it about Superman and Batman. Superman/ Batman should battle CADMUS in this film, and then end it with an Alien Armada moving into to Earth's orbit.
Do the follow up which would be produced at the same time as World's Finest, Call it "JLA". JLA should be made up of Flash (Barry Allen), Green Lantern (Hal Jordan), Green Arrow, Black Canary, and Aquaman. For JLA, I would not bring in the Trinity just yet, because if you look back at the original Justice League comics they weren't apart of it. Nor should the team actually go by JLA, but rather be a group of heroes who come together to battle a common foe... they aren't a team yet. But I would include a scene from secret origins where Jordan is bossing the others around and one of them is like "why should we do what you say you're not the leader we took a vote a long time ago that Flash would lead".
The Third Film should be "JL: Trinity", which will have Superman/Batman/ and Wonder Woman team up to battle the same alien army that was fought in JLA, only JL:Trinity will actually be taking place at the same time as JLA. This will be the Prequel trilogy.
Then, have the fourth film 1st of the new trilogy be titled "Justice League" where Superman, Batman, Wonder Woman, GL, GA, BC, Flash and Aquaman are brought together by the Martian Manhunter to battle Brainiac and the Legion of Doom; who are actually being controlled by an Alien overlord who sent his army to earth in the past 3 movies. By the end of the movie, The group of heroes decide to make the team official.
We move into the 5th film entitled "Justice League: Crisis", in this film the League will battle the Furies. The Furies should be made up of Giganta, Harley Quinn, Mera, Livewire, and Granny Goodness as well as Brainiac and we'll finally be introduced to Darkseid.
In the final film, which would be entitled "Justice League: Darkness" will have the Justice League battle Mongul, Kalibak, Brainiac and finally Darkseid. In this epic film series, Brainiac would be what the Justice League would perceive as the ultimate threat to earth, but he's actually just a puppet like Darth Vader. In fact, it's actually Darkseid who's gonna serve and Emporer type role. And he chose the furies the way he did in order to show that his power doesn't just reach through the stars but also infinitely floods the Earth as well, same way with the Legion of Doom.
The entire cast should be made of little known actors with the exception of say Brainiac, Lex Luthor and Darkseid.
For the role of Lex Luthor I would choose Billy Zane.
Brainiac would need to be CGI but voiced by 2 people to give a computer like voice to it. I would choose both Jude Law and Jane Lynch.
Darkseid would have to be played by 2 actors as well, plus be partially CGI. I would choose Brian Thompson who played Shao Khan in MK:Annihilation, to perform him physically as well as do vocals but I would also have Cary-Hiroyuki Tagawa who played Shang Tsung in Mortal Kombat overlap his voice over Thompson's give give him an extremely evil and dark sounding voice.
That's how I'd do it... tell me what you liked and what you didn't like and why.