Assembling an FPGA board on 2 layers PCB

an ep3c40f324 design i had done has passed all approvals without shielding on a 4 layer pcb with external signals of 96MHz so 4 layer is easy and can handle the additional 2,5v

you are slightly right and wrong. you can't just pick some values yu've got to place on your board. those values should be calculated depending upon the frequency response of your pcb. in fact the pcb itself is some kind of capacitor and inductor (and resistor) and has a resonace frequency at wich it turns from capacitive into inductive. so your first capacitor must have its pole theire, the next when the first turns into inductive and so on so the summ |Z| will be low enough. the |Z| depends upon the current you will need on that supply

if you just place some values you might get increased disturbance at certain resonance frequencies due to missaligned resonance behavioral of your components