I'm certainly not going to claim the years of experience that you have. And I hope I didn't insult your background. That was not my intent.
I have a Bachelor's and Master's degree in Electrical Engineering. I do all my own FPGA and PCB design (including multi-gigabit interfaces). I'm the one who spends the long hours matching impedance and trace lengths and analyzing the stackup and finding out which plane to reference to and on and on and on. I'm also the one who spends the countless hours taking return loss measurements and performing TDR analysis and fiddling with passive component values to get the eye looking as clean as it can be. I hate to use the term magic though. It's only magic when we don't understand it. Magicians are also called illusionists.
Now it so happens I have a minor in Computer Science and I exploit that knowledge to make me a better hardware design engineer. It seems this difference is what makes us both incapable of seeing things from the other's perspective. And I apologize for this shortcoming on my part.
I don't work for Altera so you'll have to pass your suggestions on to your FAE.
Is there something specific that those of us here in the forum can do to help you implement ethernet in your design (Xilinx or Altera)?