The smaller displacement engine will be smaller and thus lighter, giving more power per weight. But for the same power the smaller engine needs to rev higher and/or have a higher compression ratio, both of which might have an effect on the durability / running costs of the engine.
Larger displacement engine might also have a less steep power curve, i.e. more power at lower rpm than on the smaller engine, which could be better in something like offroad or towing applications.
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