Hmm...
Interesting responses.
So Sinister's 5,000 JLA Composite clones (with the combined abilities of Flash, Manhunter, Supes, and all of the other members of the league, but at 89.5% capacity), on top of all of the other resources, under the leadership and command of Doom, Deathstroke, Batman, Sinister, Luthor, and Detective Chimp, with 5 years of planning, aren't enough to conquer DC Earth?
Don't forget, Doom has arcane abilities as well.
He finished in second behind Dr. Strange in the Sorcerer Supreme competition (and that's canon material, not just net hearsay or hyperbole. It was in the same story where Doom and Strange travelled to Mephisto's dimension to free Doom's mother's soul).
This is Batman and Co., planning for complete DC World domination, not just JLA domination. Batman only has direct access to the JLA's genetic material and information, not that he, Deathstroke, and Luthor haven't accounted for other heroes on DC Earth. The JLA info is just what was provided to Doom and Sinister for the power sources to usurp and genetic material to manipulate because Batman has constant access to the information and trying to obtain info on other groups he's not affiliated with would arouse suspicion.
Basically, what I'm saying is take into consideration Batman, Luthor, Slade, and Detective Chimp's documented knowledge, experiences, and interactions with characters on DC Earth, but as far as resources go, Batman only obtained and supplied info he readily had access to when he forwarded it to Sinister and Doom so no one would suspect anything.
The JSA, and other DC Earth based teams that Batman, Luthor, Deathstroke and Detective Chimp have interacted with, should be assumed to be accounted for in their plans.