So wait Doomsday killed Batman , Flash & Wonder Woman happened in the comics ? Must have missed those issues ...
No. What I mean is, the JLA that took on Doomsday in the comics were pretty lame, made up of a bunch of second stringers I had never heard of until I read that particular series. Booster Gold. Fire. Ice. Maxima. Blue Beetle. Guy Gordon. I mean, granted I hadn't read a Superman or JLA comic for years, but I would have expected at least a few of the classic members to still be there. Hawk Man, Wonder Woman, Green Lantern, Batman, Green Arrow, Martian Manhunter. You know, SOMEONE. Anyways, Doomsday didn't kill any of the JLA during his rampage, even these B-Listers. Fire, Ice, Blue Beetle, Guy Gardner, none of these characters are super invulnerable like Superman. Only reason Booster Gold didn't die was due to his suit's forcefield. Even after the forcefield failed and Doomsday slammed his head in a car door repeatedly, all that did was send him to the hospital. Basically, he was toying with them, like a cat with a mouse.
So in an animated Doomsday movie, have him take on the originals (or at the very least, the members used in the television series). Superman, Batman, Green Lantern, Flash, Wonder Woman, Martian Manhunter, and Hawk Girl. Possibly even toss Captain Marvel into the mix, just to even the odds a little bit. And if they can use characters from the later episodes, like Zatanna, Supergirl, Black Cannery, Green Arrow, and Plastic Man, then great. It makes Doomsday look just that much more badass by pounding through all of them too. As he sends them all to the hospital, it ends up becoming a one on one fight between him and Superman, just like in the comics. The movie ends with Superman and Doomsday "killing" each other, and Superman's funeral.
In the second movie we have the introduction of the new Supermen. The Eliminator, who has all of Superman's powers, some of his memories, but gives no quarter to the criminal element. The clone, who was accidentally released too soon and is really just a teenager. Steel, who was once rescued by Superman and wishes to pay him back by donning a suit of armor and adopting Superman's crest. And The Cyborg, who turns out to be a genetically altered Metallo. Then, of course, the real Superman returns, but in an extremely weakened state. Once Metallo reveals his true identity, the good Supermen team up to stop him. The Eliminator places himself between Kal-El and a blast of green kryptonite radiation, transferring his powers into Kal-El, sacrificing himself to make the real Superman whole again. Then Superman kicks some Metallo ass.
And possibly do a third movie, where Doomsday returns to Earth, Superman learns his true origins, and faces off with him for round two.
The problem I have with the Superman vs Doomsday movie that came out a few years back is that they tried to cram the first two story arcs into one movie. There's just way too much, and they had to cut out just about everything from the story in order to cram it into 90 minutes. It felt rushed. Taking your time, making the first movie a JLA movie, making the second movie about all the Supermen, then possibly a third movie where we learn Doomsday's true origins, is the smarter way to go. It would be more expensive, but more people will enjoy it more, buy more copies
of all three movies, and thus they will make more money.