Well done to convert the schematic.
I'll try to answer all of your questions/observations.
* The +1.25V and +2.5V can be connected to +3.3V to save power. Due P_heat=U_drop*I.
The LM1117 has a dropout voltage of 1.3V, so the +2.5 must be connected to +5V to be able to regulate properly.
Besides, power dissipation will be the same; it doesn't matter if the heat is dissipated in +3.3V regulator or in the +2.5/+1.25V regulators.
* Howcome the many connections to the fpa isn't in numerical order?
The connections are made that way to ease the PCB layout.
* What is the value of C37 100uF/6.3V ?
Yes.
* Why is R42 present?, it's just sitting between +1,25V and GND.
R42 is to provide a minimum load for the LM1117. Just to be sure.
* Howcome (54,55,56) M1,M0,M2 is connected to VccAUX, doesn't it need 3.3V?
No, they need +2.5. All config pins on the spartan do. If you want to connect them to +3.3V, proper current-limiting should be applied.
* The 'SPI_DOUT' from the fpga and SPI_DOUT from the sdcard (via 1k) can drive eachothers output, maybe this can be resolved with an or gate or such instead?
A gate would be better. During normal operation, the SPI out of the MMC card is tristated by disabling the MMC, the same goes at the FPGA side (it's a tristate port). This way, they can share the SPI bus.
* Maybe the keyboard and mouse can share connection?, I've seen that on laptops asfair (saves i/o).
That is possible, but you still need 4 I/Os. It does save a PS/2 connector though.
* There's no over/under potential protection for keyboard or mouse?, like video output have. Howcome?
It is a minimal design. The spartan has built-in ESD protection that this design relies on. However, monitors and TV's are notorious for blowing up video ports so extra protection has been added there!
* Maybe the rs232 output of mcu and fpga can be shared without a jumper by setting an AND-gate between. Because the default level for rs232 is "1". And thus any transmission will produce "0", and if the other maintain the rs232 "1" resting state. IT should work.
Yes, no problem. However, all debug output of the PIC has to be disabled as not to interfer with the FPGA serial output.
Dennis