I am but an egg.
But I think midcow was right in many respects, a full, custom high-end system in general will be better than a 'stock' mid-end system even when augmented.
The thing is, we need to quantify how much each additional change makes, not just assume based on 'knowledge'. (What we think we know, but haven't tested).
It would be nice if we could go all Mythbusters on this, start with the stock premium system, add the sub/amp, and quantify it somehow.
I don't trust IASCA scoring so much, or 'flat' curves across the board, that really doesn't sound 'best' to me. It feels cold. I bet it's something like the folks who listened to records said when the CD revolution came about.
Sure, CD is more accurate that vinyl/analog, but they claim something was lost. Ditto with tube amps to mosfet/transistor/digital. Tube amps were 'warmer', their 'imperfections' were engrained in the mental recordings 'everyone' had in their heads.
I don't know how to quantify it except for with each individual's own ears, with their own music (the music they know and love).
I'll talk to Adam and Jamie again this weekend, they'll be at Maker Fair. (As an aside, we do the IT support for the entire San Mateo County Event Center, did the Enterprise grade WiFi over the entire 48 acre property, and we're the IT support behind the IT at Maker Fair every year. Ask Ralf Muehlen and Louise Glasgow).
I'd love to have them do this as an episode, but I'm pretty sure they still have a queue of 1000 great ideas. I'll let them use my car as the test bed, and I already have the Zapco 7-channel amp and CDT Audio 3-ways, pretty epic amp and speakers we haven't bothered to drop in yet.
My Audio guys were 'unsure' as to how clean the output was from the stock head unit. In other vehicles similar to this, they had a heck of a time getting a clean signal (even with the JL Audio CleanSweep). They're under the impression that ML has applied equalization at the head unit level, and in the amps, that makes replacing 'just' the speakers and amps problematic. They also leaned towards replacing the head unit, and I just wasn't ready to do that. I do like the steering wheel integration, bluetooth, the nav system is workable with downloads from Lexus, real-time traffic info, etc. I just didn't want to give all that away.
That being said, if midcow has replaced the speakers, amps, pretty much everything in the system except the head unit, then I think we have a valid path to move 'forward'.
So I can't give you a good answer or direction on a replacement head unit, I just haven't done the research and haven't listened to it even with my own ears, much less yours.
Let's find a way to build up a system, step by step, with an accurate way to gauge 'sound quality' that will apply to 'real world' CT200h owners. The MythBusters guys are really the best at this to be honest. I don't have the time, experience, or expertise to pull something like this off.