A good quality single subwoofer (either 10" or 12") will usually satisfy your needs and take up less trunk space.
I personally am running a single JL Audio 12W6 and absolutely LOVE the setup.
You will, however, hear plenty of opinions on different subs, different styles of music being better with certain subs and, obviously, a price range that is associated with each level of subwoofer out there. So, depends on what you listen to, whether quality or simply extreme decibals is your thing.
Back to head units:
A newer AUX capable OEM head unit and associated OEM AUX input would run you around $175-180 total.
A new ipod interface would run around the same price range. Some are slightly problematic (require being reset from time to time, etc). Steering wheel controls will be able to be used with most interface setups, which can be a convienence and a safer way to operate the ipod.
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Last edited by Jmanscotch; 06-16-2011 at 12:54 AM.