Two sensors with the same number of pixels would be compared as follows: The one with the larger pixels would take a higher quality image than the sensor with the smaller pixels. Scientists have gone crazy reducing things to digital size; a smaller sensor with the same number of pixels would, of course, require smaller pixels.
The smaller sensor may be more efficient because of its size, but it won't usually produce the same quality images as the larger sensor with larger pixels will. Miniaturization isn't always the better way to go.
Digital single lens reflex cameras (SLRs) have a better quality of image than compact or point-and-shoot cameras because they have an imaging sensor close to the size of those found on a 35mm film camera. Even the high-end compact cameras costing up to $1,000.00 use a sensor about 1/1.8" or 5.5mm x 4.1mm. Even with a 3-, 4-, or even 5-megapixel sensor, they can't create photos comparable to the 3-megapixel SLR.
Because the technology is relatively new, many customers are confused by pixel numbers, and manufacturers aren't completely upfront when the talk about pixels either. A camera with 4.3 million pixels may only use 4 megapixels to actually record light information for the image. These are described as the "effective" pixels, and you have to look really hard to find where the manufacturer discusses these in your manual.
However, this is the number you want to use when deciding on the camera's pixel size. If a camera has 3.1 effective megapixels, yet is advertised as a 3.3-megapixel camera, it is still only a 3.1-megapixel camera.
The law requires that the effective pixel count be advertised along with the pixel count, but this isn't always true, so look for it in your cameras manual.