I have followed all the guide lines for powering up the Cyclone IV. However, the 3.3v Regulator is heating too much and also the Cyclone IV FPGA. What's wrong with my schematic? Is there a problem in connecting the heatsink located below the Cyclone IV chip into 1.2v? By mistake I connected it into 1.2v line.
Internally, the pad is electrically connected to the device GND pins, so connecting it externally to anything else is a critical error.
The Intel device page has a link to a packaging spec list, that links to a packaging spec page, that links to a pinout document, that has this footnote:
(4) The E144 package has an exposed pad at the bottom of the package. This exposed pad is a ground pad that must be connected to the ground plane on your PCB. This exposed pad is used for electrical connectivity, and not for thermal purposes.