I have to say that I am pretty impressed with the stock system. There are most certainly better sounding car stereo's out there, though only a few of them are OEM. But, on the whole, I can't really complain about the sound quality. I have always looked at BOSE as producing systems that sound good, not accurate, meaning the sound is manipulated and differs from its source. This is the first BOSE that I feel comfortable saying is pretty accurate. The vocals are clear and well placed, the highs are not fatiguing even at high volume levels, the 9" mid-bass/sub's in the front doors help to reinforce the sound stage, while the 12" sub in the rear deck adds to the low frequency response. The sound is well balanced, and enjoyable to listen to. I know it lacks some of the detail that is present in some of the more expensive OEM systems, or in well tuned after market systems. My hesitance about making modifications to the system is the fact that with all the DSP equalization that is done to match the door speakers to the dash speakers, the cut off points for the mid/high to mid-bass/sub to sub, and not to mention the rear door full range speakers; there is alot of work to keep the coherence of the factory system if you make changes to the speakers and try to add amps. I know that previously BOSE was using speakers with an impedance of .5-2 ohms, which makes it difficult to find speakers that would work well with the built in amp.
As I am sure those of you who have built systems know, changing the speakers from 2 ohm to 4 ohm isn't going to hurt anything, but will limit the amount of power available from the factory amp. Assuming the speakers have the same sensitivity, say 90db/1w/1m, and 64w peak at 2 ohms at the amp. Changing the speaker to 4 ohms would reduce the amps out put to ~32w peak, would lower the max output of the speaker by 3db, which doesn't look like a lot, but reduces perceived sound by half. Which in turn reduces the potential dynamic range of the music, unless you are listening to Metalica's latest release

. It can also introduce distortion because the speaker isn't receiving the power it needs to physically produce sound. Granted this should only be notice able at higher volume levels, but it is something to be aware of.
I am all for doing what you want to the sound system, its your car, and there is a reason why there are so many different makes of speakers and amps, everyone likes a slightly different sound. For me, I am happy enough with the sound system that I don't want to mess with the issues of possibly loosing the DSP features, or introducing more distortion. I look forward to what all everyone finds out about the current system, and what you all do to address it's short comings, and your own take on what is the best.
~ Matt.
Side Note: I do hate the quality of the sound on XM.... Yuck... I only use XM for the comedy stations and when I am driving and there is no real radio stations to choose from... Thank God for the HDD and iPod connection...