My experience is that you cannot find one answer for your qesution
because you will find that in some designs Xilinx is better, but in some designs Altera is better.
Why do you need to know the difference. Once you choose the FPGA, the PCB layout will be bounded to the one you select. And the pin assignment will be different. There is no chance for direct replacement between Xilinx and Altera.
So there is no correct answer for such kind of question.
If your design is generic (without using the IP designed for Xilinx or Altera)
You can P&R the design and share your finding.