The biggest complaint about quartz products is that if something does manage to scratch or somehow deface the surface of your counter top, it is almost impossible to repair. This is because engineered stones have a surfacing substance applied to them.
With granite it is possible to repair a chip or fill a scratch and to cover your tracks by surface polishing the material. Afterward the repair can often be unnoticeable. This is something that is difficult or impossible with many engineered stones.
Granite counter tops occasionally need to be sealed because they are actually porous. Also over time each color of granite will tend to shift (get one shade darker or lighter, change hue slightly) as it is mined from deeper and deeper in the Earth. So if you ever wanted to replace a piece or add to your job, the odds become increasingly thinner and thinner of finding a good color match, even of the same color.
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Source: http://knol.google.com/k/natural-stone-granite-vs-engineered-stone-quartz#