Custom units/commanders - assigning cost ?

Well if you took away all their magic and their holy (but left their sacred) I'd consider 250ish. They lost a total of 8 Magic Levels (including the Holy) and now are regulated to being on-land without the help of a magic item. Though for Niefel this might be too low. Since they could churn them out and equip them with a Rainbow fairly quickly and cause alot of havok with minimal cost (250 Gold and a Wraith Sword would probably do the trick fairly well, Boots of Quickness, and a Ring of Regen would complement it nicely).

The cost dependant on the nation is primarily a "What would Zen think" and not a "Game mechanic" argument. The Nations I like use all their troops just for different purposes or different combinations. Thus if you had a big beater like the Giant I'd hope the cost would be modified with how easy it is to abuse and either adjust the stats or the cost to make it balanced vs opponents and in the internal structure of the nation.