You can take a look at what Tom's Hardware said in their review GeForce GTX 690 Review: Testing Nvidia's Sexiest Graphics Card
Benchmarking Nvidia’s new GeForce GTX 690 almost wasn’t even necessary. The company gave us a great idea of what to expect when it told us that its new Death Star would be fully operational, featuring two uncut GK104s. A slightly lower base clock suggested average performance just a smidge below two GeForce GTX 680s—but certainly not enough to be noticeable while you’re gaming.
If you consider $500 for GeForce GTX 680 to be a fair price, then $1000 for GeForce GTX 690 is comparably reasonable. But is it any better? Or should you just stick to a pair of Nvidia’s fastest single-GPU cards?
That’s going to depend on your priorities.
Practically, two GeForce GTX 680s facilitate slightly better performance and they exhaust all of their heat out into the surrounding environment. They’re also scalable at a more granular level. That is to say, if you buy two GeForce GTX 680s today, you could add a third tomorrow and be out-of-pocket for $1500. For most enthusiasts with the right motherboard slot configuration, that’s the smarter play.
...And so we come full circle. Nvidia’s new flagship is a lot like an expensive sports car: attractive, exclusive, and not necessarily practical. But if you’re in line for one, there’s a fair chance you already know that and probably don’t care.
In short, the two GTX 680's are better in performance. But, the 690's are less in heat.
Hope that helps