Because it's more expensive, you can get two 680 gtx for 900$ vs a single 690 gtx at 1000$, performance wise two 680 gtx are slightly better than single 690 gtx.
The good thing about the 690 gtx is the power consumption, heat and it's the coolest(in looks) single card.
Two GTX 680's cost less, and tend to overclock significantly better than a GTX 690. This makes it perform better too.
So, cheaper and more performance.
Unless the user has severe spacing issues, and wants the insane performance whilst only having one card on their motherboard. Two 680's is a much better option than a single GTX 690.
It is a lot of money for 2x680's or 1x690 - many folk going gown this green route clearly don't have many issues with money (power consumption - so much for 'green' route ) and therefore want the best return (higher fps). 2x680 marginally wins here.
Single card GTX 680 systems are popular because the single card is still capable of handling virtually everything you throw at it. And when it comes time to replace the card, there will be undoubtedly more powerful single-card GPUs available that can handle the job.
Having two 680's in SLI is a more popular option than the 690 for reasons already mentioned: Generally better performance for less money and less overheating issues. Plus, with cards in SLI there's more space between the cards and therefore cooling solutions are more effective.
Not many want to pay a cool grand for a card that will be outdated in 6 months because of the next big thing out. A single 680 will run most everything on max settings just fine unless you game on 3 displays. A single 4Gb 680 runs all games very fast without stutter on my single 30" 2560 x 1600 display. I could get a 690 but dont see the need just for gaining 20 more unnecessary frames per sec.
And the if we compare a single GTX 680 and a single GTX 690. What will happen ? I think that GTX 690 wins here. What are the prizes around the world for an original GPU's. I found one GTX 680 for 1737,28$, it is very expensive why? And I cant find any GTX 690's around here, and if I find one it will cost 3000$ for sure.
Dual GPU values plummet even faster than single GPU's when a new generation of cards come out, and can actually be rather hard to sell. The real only advantage of a dual GPU card is the lower power consumption, and being quieter and cooler.
I have a GTX 690, upgraded from gigabyte gtx 570 s'oc. It is a great bit of kit and overclocking is simple. yet I have no game that actually needs to be overclocked for. Bf3 ultra all down the list ang It runs great.