Hmm... I think 6x9s are built to give a certain amount of bass... more than standard 5.25" round speakers anyway. In fact, in a way, bass is what theyre all about. 6x9"s and 7x10"s are the closest thing to a sub you can get while still working with speakers with a smaller cone area/mounting depth. To your average Joe, 6x9"s produce a lot of bass. But whether they deliver acceptable SQ is a different matter altogether! Basically theyre all right for someone wanting to upgrade from a basic factory system, but not really a big SPL or SQ fanatic, and wanting a better, more powerful sound accross the frequency spectrum, but without forking out for separates. But they are no substitute for nice components and a sub.
Thats my tuppence worth anyhow!
Now regarding the lack of bass, I understood it that you meant not just that the bass was lacking a bit in the sound, but that there was a real problem at the lower end that meant you were getting no bass from them at all. This isnt due to the inherent weaknesses of 6x9"s but some other further fault, wither with the speakers or the setting up. If it affects both, my guess is theyre out of phase. If it affects one mroe than the other Id say theres a good chance theyre blown.
If theres a lot of distortion, but only when you turn it up, Id look at the amp, cos it could be clipping.
In general those JBL GTO series 6x9s are reasonably powerful, and should be packing a fair amount of bass (maybe not sub-bass but still what one would term bass) so Id have another look at them. Even try wiring them up to a mates system, etc. to test them.