First: Voyager is FAR from being Star Trek, despite the name saying otherwise.
Anyways: On spaceships, it is a problem of "Where the heavens do we put all the stuff we need for Matter/Antimatter-Reactions?"
Second: Voyager is far from *regular* supply by Starfleet standards, resulting in shortages of energy.
On Planets, the Federation uses "standard" Fusion reactors (The Ka-Boom is not too big if something goes awfully wrong) to produce energy. And with enough water on teh planet (or anything small enough for fusion-reactions), the supply shouldn't be the problem.
Another question is: How much energy is actually lost? Nucler reactors of our time loose about 95% of the produced energy, with still *very* large outputs.
something tell's me, that this ratio can be improved.
And a replicator works like: You take a bit of energy, create a bit of apple, and repeat until it reaches the specified size. Look it up in the Technical Manual for the NCC-1701-D Enterprise.
So who's the geek here ;-)
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