SInce yesterday Element14 offer custom builds of Rpi! More information can be found here:
What you want to include to your dreamed Rpi? For me will be nice if:
- all ports are placed of one side
- have more GPIO pins
- more RAM
- integrated WiFi and Bluetooth
- integrated Storage (fast one)
- Gigabit Etherner
- and USB3 (if it’s possible)
But from what I’ve read this customization service is only for big orders 
which is shame…