As of right now I'm going to use the factory stereo. Only thing I'm changing is the door speakers and rear deck speakers. I have the alpine mrp m500 pushing my alpine type r 12 sub. i have the alpine 6'5 component door speakers and pioneer 6 x 9's. thinking about buying alpine 6'9 to match everything.
Its just a pretty moderate system but sounds pretty great.
Ran from the head unit speaker wires into an MTX RE-Q5 (Keeps the bass level constant. As you turn up the volume on modern factory headunits they drop the bass to protect the crappy factory speakers)
From the MTX ran into an Alpine MRV-F340 4 channel amp.
Amp is powering Alpine SPS-600C speakers (6 1/2" with tweeters) up front. Didn't replace the rears yet and they are still running off the radio power (they'd probably crap themselves pretty quickly if I ran them off the amp. Probably will replace them eventually which is why I got a 4 channel amp)
The RE-Q5 has sub outputs, and those are running to a Rockford Fosgate 2 channel amp powering my 2 old 10" Kicker Impulse subs.
You got some plans? I'm going to post pictures when I'm finished, planning to build a set of corner boxes for the subs like SubThump offers. right now they are in my old box I build, just a single box in the center of the trunk.