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In gears, the Zohar is "occupied" with the Wave existence, which has been trapped in there for god knows how long. but in Saga, U-DO's just there, he doesn't really do anything, and he has no desire of being freed at the end of the machinations of his plans. Almost all of the events in Gears where orchestrated by the WE for that sole purpose. U-DO however, is not trapped,, he exists on a higher level, and the Zohar merely serves as a way for him to connect with mankind.
The ES would also be useless, since their main power source, the anima vessels, is gone. Even if they develop a new engine like they did for Asher, they still won't have the same power as the omnigears.