Cyclone III not configuring

I don't think just having VCCA at ground should hurt anything. I would suspect that the center pad isn't making contact. The center pad is the ground return for the core. The ground pins are only the port driver and PLL grounds.

I've soldered other parts with a ground slug and it takes a LOT of heat to get the board and plane up to temperature. If you're hand stuffing boards the hole is a good idea. If you are going to stuff more boards I would only solder 2 pins to hold the part in place and then solder the ground. With only two pins soldered you can verify that the ground slug is soldered in place by trying to wiggle the part around. Once you know the ground is soldered then do the rest of the pins.