I installed mine in a '98 Jetta, using the same wiring method. I get acceptable bass. When my wife's in the car with me, she keeps the volume rather low, and I have a hard time hearing the low end (which is really no surprise, as I think I'm a bit deaf in that range anyway). However, at what I would deem "acceptable" volume levels (about midway in the volume range on the head unit), there's plenty of bass. So much so that on some songs I feel the urge to turn it down, as my amp can dish out more than my speakers can take, and I don't want to blow them.

And this is with my rear desk speakers not sealing the deck holes, which would actually decrease my bass somewhat.

Is it possible your amp has a built-in crossover and you've just got it set wrong (i.e., filtering out the low end)?