Resurrecting a thread from the dead here...
The factory head unit, including the way the system is wired, leaves a lot to be desired.
I'm 2 months into ownership of a gently-used '04 King Cab XE.
As far as audio is concerned, at first I blamed the factory (non-Bose) head unit. I replaced it with a Kenwood head unit (KDC-BT762HD), which helped but the sound still seemed lacking. I had nearly convinced myself that the tweeters were baked until I pulled out the schematic in my Haynes manual...
THEN... I found a big piece of the puzzle:
The factory wiring for the two-door Frontier puts the door speakers on the rear channel and the 'premium' A-pillar tweeters on the front channel. Maybe the Bose head unit makes good use of that configuration, but the factory head unit can't. My Kenwood couldn't either.
I managed to flip it into something totally Kick by rewiring the factory outputs to put the door speakers and A-piller tweeters on the front channel, then adding in a pair of surface-mount speakers (Pioneer TS-X150) on the rear channel.