Description
No, Stratix® and Stratix GX devices are not pin compatible or migratable between the two different families (although they have migration capabilities within their own respective families).
The most obvious difference that prevents pin compatibility across families is that Stratix GX offers transceiver blocks on one side of the device while Stratix does not. Additionally, though the IO banks of Stratix GX (other than those that contain the transceiver blocks) have similar functionality to Stratix, the pins in these banks are also not fully compatible. Issues such as routability and vertical migration within the Stratix GX family required pins to be placed in different locations than they were in Stratix.
For a full list of differences between any two devices, you should check the available pinout files of the Stratix and Stratix GX devices in question.