While the inputs vs outputs will give the best indication of the direction of the subjects' weight, I think it's important to consider where the deficit calories will come from. In the first scenario, the calories for John may come from fat storage more than Joe due to his sugar consumption. One also has to consider insulin effects, etc, which I don't feel qualified to answer.
The second scenario probably depends upon the intensity and % of muscle used to calculate the metabolic effects of the anerobic vs aerobic exercise. However, during a 24 hr. period, if both have an identical caloric deficit, then one must answer where the additional 1000 calories came from. Conventional wisdom would say that the aerobic exercise would be more catabolic and thus the calories would come from breaking down some muscle tissue (in addition to glycogen, fat, etc.). However, I'm not sure if this is a correct assumption.
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