It sounds like I had some of the same thoughts and concerns you bring up.
In the end I came up with a very different solution than I planned in the beginning. Sorry this post is long, but you may be interested in how I did this and my reasoning.
What I wanted:
Sat Nav, satellite radio, and hands-free Bluetooth connectivity--all without a rubbish looking aftermarket solution. The Double Din Pioneer units you mention looked like viable options. However, upon further investigation I could see some potential problems down the road, which included the issues you raise.
The Problems:
(1) I was a bit uncomfortable about giving $2,500 to some run-of-the-mill shops with uncertain skills so they could thrash about under my dash. The high end shops with clear experience doing this to Porsches were even more expensive.
(2) It appeared enough hacking was required it would be difficult to go back to OEM---something that does matter to many people. Moreover, the installation options suggested by several experts placed the re-located controls in less optimal positions.
(3) To me the biggest issue is that I have come to believe even the high end Pioneer systems may soon become antiquated and need to be replaced with something very different---or perhaps worse, just wind up cluttering the dash like a 21st century version of the old 8-track players from the '70s. Specifically, I'm thinking about the emergence of Google Navigation for cell phones, Pandora, and voice command apps.
My Solution:
The key weakness of using a cell phone for such applications is rapid battery drain and I did not want to use an ugly cigarette lighter mounted phone charger with its unsightly wires always dangling over the controls. To get around this, it was easy to pull the radio and place clamp-on splice jumpers on the switched power leads without cutting any wires or altering any cable harnesses. With the functioning radio back in the dash I fed the DC voltage source to a small phone charger that I secured under the dash. A very simple adaptation of a $10 snap-in belt clamp for my phone allowed me to mount the phone in a convenient and visually pleasing location on the dash. Even though it mounts very securely I can pull the mount on or off the dash without any dash modifications and it doesn't require any of those awkward and ugly aftermarket solutions (suction cups, clips, clamps, widgets that plug into the cigarette lighter, glue, magnets, or rubbish that precariously clips objects on the vents). The coiled power line to the phone is very unobtrusive when in use and retracts out of sight when not in use. For short trips I usually don't plug it in. In order to gain wireless access to the audio system I use a Motorola T505 bluetooth adapter. It works very well, is quite small, and mounts wirelessly on the the sunvisor. When sitting behind the wheel one doesn't really even notice it. With an overnight charge I find it works for many weeks.
The result:
When I get in the car I snap my Android phone in the bracket and touch a button to activate the Bluetooth adapter. The phone automatically handles the satellite navigation and speaks through the car audio system. I used to pay for X-M satellite radio because I like the variety and hate commercial-laden radio. On this basis Pandora is superior and free (or nearly so). If a call comes in while Pandora is running, it will pause until the call is done. At least with my phone, the sound quality is quite good. Similarly, when Google Navigation starts to speak, Pandora automatically pauses and then resumes when the navigator is done speaking. An inexpensive voice-confirming Android app allows me to voice dial for outgoing calls. Google is frequently sending out automatic cost-free upgrades for the navigation app. Moreover, since one is linked to the web, information is always automatically updated and a street-view of your destination pops up as you approach. The radio and CD player still work with a touch of a button.
In the end for less than $100 it was possible to configure a clean system that has few drawbacks and in several ways is superior to a >$2,500 "Pioneer solution". Perhaps most important to me is that the dash remains uncluttered and completely OEM. The capabilities of cell phones to do the work of these big, expensive in-dash Nav/audio/bluetooth systems changes by the month. No car maker or aftermarket audio system manufacturer can keep up with this pace. In a couple of months I will get a new phone that will be much faster and have many more voice options. You should be able to do the same thing with any other standard smart phone. When I do upgrade, all I'll have to do is get a new belt clip for the phone and I'll be set--and I won't have deal with any dinosaurs in the dash.
Hope this is helpful. If you need more details please let me know.
Dave