The reason I upgraded was because I wanted an 6-disc in-dash changer (they don't make these anymore) and the MP3 playback (2003-2005 4Runners don't have this). Compared to the stock headunit, the Scion units put out a better range, the clarity is much improved and the bass is pretty good for something that's stock. It's perfect for people who want something that plugs right in and improves the sound over the stock headunit. But if you're an audiophile, it will leave you desiring something more. I personally think it sounds great for something that only required me to unplug my old unit and plug this one in. The flexibility of it is pretty good, you can pick between tC, xB and xA models within the headunit as well as Neutral, Feel and Hear modes. So you can play around with them and pick what you like the best.
BTW, you can't install the Scion unit in a JBL-equipped 4Runner without modifications.
Having said that, I recently plugged in a JBL Nav system with a digital JBL amp from a Sienna and it sounds much better than the Scion unit I have.