Need some advice about selection of FPGA devices(probably with PCIe interface)

Full length cards should fit in a desktop case, but in many the metal support for disks (etc) comes down too far and fouls the end of the card.

In a cheap case this can be fixed by drilling out a few rivets and bending the support out of the way.

The other problem is the lack of airflow around the expansion cards. With cards drawing 20 watts you need some additional forced cooling between the expansion card slots.

If you want to connect to a mobile device, about the only simple connection is USB to serial - ok provided the data rates are low.