I should also point out that these mutual exclusions only apply within a single city. So you can make it so that two National Wonders within a group are mutually exclusive, but you can't make it to that you can't build Wonder X if you already have Wonder Y somewhere else in your empire.
It still has some very nice uses for National Wonders; in my own mods (specifically the Empires mod), I created four National Wonders in a mutual exclusion group: Wall Street, Hollywood, the Red Cross, and the Three Gorges Dam. So four of your cities will end up with these, which basically causes the cities to specialize a bit (Wall Street making one city your financial center, Hollywood making a cultural center, and so on) and each also has empire-wide effects. It's really a very under-utilized bit of functionality, and could have made the vanilla game much more interesting.
Now, if you DO want something more complex, like having a Wonder lock out a different Wonder from every city, you can use the CanConstruct function in Lua to override the process. In theory there's no limitation to how complex the triggers can be, since Lua can cover a lot of different algorithms. But don't use these Lua overrides too much, or it'll slow things down.