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1. Additional weight
2. Takes more battery power
3. The display is crap comparing to Retina, so there is no need for it at the first place
4. Apple should distinguish somehow between its laptop lines - the discrete graphic card is one factor to do so
5. There is not space to put it; thus, the physical size of the air would increase.
 
To build a laptop that thin they've got to make sacrifices somewhere. It's got nothing to do with the screen (crap or otherwise), if that was the case the rMBP 13" would have a discrete card; it doesn't.
 
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