My 08 Prius (JBL/NAV) had all speakers replaced, couple of Focal amps installed, sub, JL Cleansweep and summation unit. I was curious if anyone did something similar, and then later added an aftermarket deck in the empty slot below the OEM head. If so, did it sound better? Although my system sounds good, something's still not quite right. Not so much the quality of the individual sounds, but rather how everything is blended. And, I've had it tweaked to death by an expert using microphones and EQ analyzer/scope thing (do not know what else to call it). I would imagine the issue would stem from the type of signal that is fed from the OEM head unit to the Cleansweep. Maybe an aftermarket deck would without the Cleansweep would produce better results.
Your Cleansweep gives you the perfect point to jump in with clean signal from an external device like a portable CD player or MP3 player. This will essentially take the factory head unit sound quality out of the equation. See what you think (sound-wise) when piping in audio from something else whose sound quality you trust. If it's noticible and you like it, then you have your answer...if not then you can start looking at other components/factors.
Won't it be a bit different because with the head unit, I will no longer need/use the JL Audio Cleansweep and summation device?
No ssi needed, you could even skip over the cleansweep and run RCA cables directly from your external devive into your amps, but I believe the cleansweep dsp has a single set of RCA jack inputs, which would simplify splitting and spreading the signal across all channels.
As usual, I went off and did what I wanted, lol. I had an Alpine 9886 deck installed below the OEM unit. The JL Audio Cleansweep and Summation units were taken off. The improvement in sound is staggering. My system now sounds incredible (as it should!). In hindsight, I would've only kept the Cleansweep if I just wanted to go with an OEM head and no amplifier.