I've been researching this major choice as well, and agree that there are some very powerful aftermarket options that quite easily rival and often exceed OEM's specs. The differentiating features will be plus-es for some and irrelevant for others.
For example, the Pioneer Z1, when it comes available, will offer:

Bluetooth phone integration (including Nav & handsfree calling to any of your contacts),
Mute of car speakers for all Nav Instructions & Calls
Voice commands,
XM Radio,
XM Traffic syncs,
30GB HD drive that can burn tracks direct from CDs onboard,
11 Million POIs (with phone #s if avail)
Intuitive Route- Learning
Onscreen DVD-playback (with workaround for while-driving if you want),
Touch-screen (this is one of my MAJOR issues with OEM- I've used touch-screen nav's for 3 years, and can't imagine going back to buttons),
AND steering wheel integration for stereo functions via a PAC module.

All of these features can be had with aftermarket at much less cost & headache than the OEM. BUT as far as I understand you'd lose the On-Board Computer with a double-DIN system, unless you do a creative work-around to install it elsewhere (like low center console), which may be more "custom" than some owners want.

For me, this loss of the OBC is the only thing holding me back from installing such a system. Probably not a deal-killer, but just something I'd like to test-drive or see in person before doing it on my X5. I'd even consider a single-DIN flip-up screen (like the N2, I believe) to avoid losing the OBC, but that's just me.
Hope this helps & I look forward to more conversation on the pros & cons. It'll help a lot of us make up our minds, I'm sure! Thanks for posting this!
M