Pace
I dont think I really mind any combination, but it seems to me if the cockpit is glass the more elements that are combined the better. The earlier G1000s and Avidynes had seperate autopilots and the Avidyne, 430s and a conventional transponder. It made sense to combine these if only because you are dealing with a single piece of kit. Of course from a redundancy view point it may make less sense - with a pair of 430s at least you know that is enough to get you home if both screens fail.
I am not sure how reliant or not you become. It is true that it becomes more difficult to go back to a conventional cockpit because the information at your finger tips is unsurpassed. Gone will be the moving map, the plates, GPS (although not many will fly without GPS of some sort these days), traffic, etc. There is no doubt in my mind flying an IAP with a six pack is a much more difficult task.
In that respect some basic skills will be quickly lost but I am inclinded to say - so what, if that is what you fly so be it.
Of course I agree when the whole lot packs up it is a different matter but in the event that the whole system fails, you are not left with very much anyway - it is a real emergency.
At the light GA end in VMC even with the most integrated glass you are left with a AI, compass and with luck a radio and hand held GPS from your flight bag. That should be more than enough, and if it is, some sole searching of basic skills is warranted. A complete failure in IMC is a different matter; clearly it is well worth rehearsing what you would do, but at the least almost certainly it will involve getting as much help as you can from ATC and landing as soon as possible.