Following some info from a few people on groupdiy (Designmasta and tmbg) I've had a look at the Xilinx range of CPLD's - and I must agree, for more advanced boards (i.e. a next generation board of this type?) then a cpld is a definite possibility.
I think the main use of a CPLD in a board of this type is more a routing matrix for now though, or possibly a routing matrix with some extra functions.
Programming them looks relatively simple (you need a parallel port on you're PC from the looks of things, and the right cable that comes with the $50 starter kit).
Anyway, I'm hoping to sit down tonight and do the schematic updates discussed.