The single biggest thing that determines a waja's value is its generation. Since customs are only available through the purchase of CWP, generation 1 wajas are worth the most. Each generation after that is worth less, though after some point wajas start getting expensive again. Wajas of gen 100+ seem to be worth quite a bit, and are known as super gens.

I personally think that the super gens will come to a point where they are worth as much as any other waja, simply because you can always make a higher generation. One generation 156 waja can have as many 157 generation pups as the owner desires. However, you can never go backwards. You can never breed lower generation wajas, so their value will always stay the same.