The time sync and the sensors don't sound all that interesting to me. The I have a lack of knowledge about the time sync advantages so it might be good but I just don't know enough. There are already a ton of sensors for the Arduino -- there isn't really a need for more.
However, the FPGA connected to pci-e would be outstanding!
In many ways I have the opposite perspective of AlexanderMerz. Intel has positioned Galileo as an Arduino. This attempt at being beginner friendly has caused it to be far more limited than it otherwise should be. I like the Arduino headers for hardware compatibility but this is a powerful board behind the beginner-friendly facade. There are already plenty of excellent Arduinos that are beginner friendly we don't need another. But a system that is powerful while still fitting into the budget and design tool limitations of a hobbyist is very cool. FPGA? sign me up!
I don't know what I would use a FPGA for, but I would love to play around with having one connected to the Galileo. It would help with IO and would be pretty unique. Galileo's pci-e port, while being unique and very capable is currently mostly going unused. WiFi cards can easily be done via USB. It would be nice to have a better use for it.
My suggestion is to try to find a way to add on a HDMI header to the FPGA. There are ways of doing HDMI out with a FPGA. Having video as an option would add a lot of value to the system.