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Increases in aperature increase not only resolution (up to the limit of the night's seeing) but also increase lightgathering. Increased lightgathering means you can run your camera on shorter exposures which help "cut through" the atmospheric light scattering by better capturing those short instances of good seeing than longer exposures will. Increased lightgathering also means you may have sufficient light to be able to used coloured filters to improve the apparent seeing and still run short exposures.
Longer focal length means greater magnification and larger image scale but you can get the same effect with very little light loss using good quality barlows or powermates.
So given a choice between increased aperature and increased focal length I would go for aperature, assuming that the quality of the optics is the same of course.
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