Yes, the GT 640m LE is much better than the 6470m.
Yes, the 20GB SSD is better than no HDD, but the Lenovo Y480 has a standard voltage quad core i7 with higher clock which will give you a lot more CPU performance in both single thread and heavy threaded application. Replacing the HDD with an SSD or hybrid drive is much easier than replacing a CPU (if it is possible). Unless you need a low voltage CPU for battery life, there is no reason to get a much slow i5 instead of a much faster i7. And that too can be solved by having extra stick of battery.