Final Crisis is the perfect example of great story ideas but various factors such as being far too short (killing much dramatic tension and creating massive confusion), massive delays, poor editorial decisions, etc.
I've often thought long and hard on how Final Crisis should have gone:
1. Doug Mahnke should have done the art throughout the entire series.
2. Countdown to Final Crisis should have been guided by Grant Morrison with Paul Dini, Geoff Johns, Tony Bedard, Jimmy Palmiotti and Justin Grey, Peter Tomasi, Gail Simone, Greg Rucka on writing duties to properly set up Final Crisis. You'd have each writer write just a month (or two) of scripts as opposed to everyone writing at the same time like in 52, so that way no one writer would be overwhelmed.
The story would be Darkseid manipulating the Monitors, Superboy Prime, and Monarch, fighting the cosmic war in which evil won, ending with Darkseid's "death" so that the Fifth World would be created in his image.
In order to prepare the Earth for his Fifth World, Darkseid chooses Libra to create a new Secret Society of Supervillains. Their main task with the Sheeda is to kill the New Gods who have chosen to live on Earth (Mr. Miracle, Big Barda, whatnot) and to take control of the Spectre.
The Search for Ray Palmer throughout the Multiverse would have Hawkman, Ryan Choi, Adam Strange, and Ray's Teen Titans.
There would be no Jimmy Olsen, no Piper and Trickster, no Jason Todd, Donna Troy, and Kyle Rayner, no Harley and Holly, and no Legion of Superheroes.
3. It should have been longer to better develop ideas particularly Darkseid's machinations and the Multiverse.
4. It should have focused on a specific set of characters:
- Superman travelling throughout the multiverse gathering various Supermen giving some dimension to the DC Multiverse, instead of Superman just popping up and showing bizarre universes where everyone is black, or simply Nazis, and whatnot. I think Superman trying to recruit Ultraman, Captain Marvel, Captain Atom, Uncle Sam, Mister Majestic, Red Son Superman, Kingdom Come Superman, and whatnot, would be cool.
- Batman struggling with his imprisonment by the New Gods. His efforts, while failing to kill Darkseid and leading to his death, would create massive setbacks for Darkseid helping the resistance find victory.
- Barry Allen coming back. Really the guy comes back and you don't have anything dealing with him going "I'm alive!? How?"
- The Martian Manhunter and his death. Signalling the first strike of Darkseid, Libra and the Society, and the Sheeda against the DC Universe after Darkseid's victory over New Genesis. The Martian Manhunter would have gone down like he did and the heroes would mourn like in Final Crisis: Requiem as opposed to just a few panels that he got in Final Crisis proper.
- Aurakles and the Seven Soldiers (Shilo Norman, Zatanna, Manhattan Guardian, Frankenstein, Yistina, Bulleteer, and Klarion) trying to form a resistance against Darkseid's Fifth World. It would be a small resistance having Green Arrow, Black Canary, Supergirl, Ray Palmer, Red Arrow, Speedy, Connor Hawke, Vigilante, Halo, Stargirl, S.T.R.I.P.E., Barry Allen, the Crimson Avenger, Wing, and Mr. Terrific. Everyone else on Earth would be imprisoned. So the odds are completely against them until Batman's efforts allow the Green Lantern Corps to arrive on Earth and Superman returning from the Multiverse with the 52 Supermen.
- And Wonder Woman leading the Female Furies (Mary Marvel, Starfire, Power Girl, Donna Troy, Wonder Girl, Hawkgirl, Raven, and Jesse Quick) under Darkseid's control.
Those characters should have been given the focus instead of Morrison trying to cram in everyone from the DC Universe in for the sake of having them. Just like in Crisis of Infinite Earths where while everyone was in, the focus was on Barry Allen, Harbinger, the Supermen of Earth-1 and Earth-2, the Monitor, etc.
5. No Mandrakk, seriously WTF.