The more pixels a camera is able to capture the more information is available for processing later on. So I think you should concentrate on pixels. The size of the sensor is going to affect the focal length. For example, a sensor that is 1.6x magnification factor is going to turn a 100mm lens into a 160mm lens. There's also a point at which megapixels becomes an over kill and not worth the extra $$$. My Canon D30 shoots at just above 3 megapixels and I've been happy with prints made at 4x6 - 8x10s. Most should be happy 6 megapixels.
Don't forget that megapixels is not everything and does not make the picture. The camera's functionality and quality should be evaluated as a whole. Don't pass up a 6 megapixel camera for an 8 megapixel camera just on specs alone.
Also consider the cost of memory. The larger the image processed the longer it takes for the camera to cycle and write to whatever flash media is being used.