Some top politicos are now urging the Gov to reach out to fuel cell mfrs. 
Ford was mentioned, with a potential billion dollar investment. I 
mentioned this group's talent pool for developing a controller (forgive 
me).

Some serious work is being done on embedded Linux systems. Real mode 
kernels are being used. Most development is focused on small appliances. 
A large process controller would not be so constrained.

My feeling is;

1) Use protected mode, multitasking Linux PC to "manage"

2) multiple real mode Linux x86 add-on cards.

Quite a variety of x86 embedded cards exist. Some are complete 486 
computers on a chip with full I/O, memory, etc., and plug into ISA slots. 
Perhaps DOS could be used for the embedded card? Lot's of questions!