If you're talking about cost per seat-mile, I'm sure the short flight has a significantly higher cost relative to the long flight (assuming they're both on AA mainline aircraft, not RJs).

Meals, when served, average between $6-8, so that's not that big of a deal.

Assuming the same aircraft and load, you'd still need the same crew size, though you'd have to pay them for more hours, but nothing on the ground is really affected by flight length (e.g. ticketing/res support).

Overall, I'd say your top three biggest differences are fuel, crew hours paid and meals.

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