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Does your commute have much highway driving, or is it all city?
Generally, manual transmissions have shorter gearing than their auto counterparts, with the exception of "eco" trims like the Civic HX/hybrid 5MT's. Autos have more drag/loss in power, but the taller gearing can sometimes more than make up for that on the highway.
Frankly I don't know much about the Malibu's hybrid system, but I'd be inclined to go with the MT model myself. Hybrids only make sense to me if they're also downsizing the engine, which is not the case here. I wouldn't worry too much about the battery though; northern hybrid batteries last a lot longer and they'll generally last more than a decade anyway.
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