f/2.8 and f/3.5 are the maximum aperture of the lens. The Canon lens listed allows 2/3rds of a "stop" more light than the Nikon you mentioned. 2/3rds of a stop isn't a lot and could easily be accounted for by adjusting your ISO or shutter speed.
Both of those lenses are very sharp. I wouldn't necessarily base the camera purchase decision, that's going to lock me into a system, on a macro lens. Buy the camera that you "like" more. Really.
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