Having just bought a 2010 Pathfinder SE I went through everything you are asking.
1) ok no experience in this but as far as I know the ride is the same.
2) I went with Digial Bose system, NO navi because I wanted to add my own. After research, there is NO way to add a deck to the 2010 models because of the change in dash arrangement. (as of yet)
If you want navigation, buy aftermarket dash unit or spend the extra bucks for the stock navigation.
Yes you can custom something but unless you're proficient and DIY, it will cost $$$. (see thread with carputer)
SUBS- the stock bose with 8" sub was good, but not good enough. I like my car to rumble. I had 2 Alpine type R's and an Alpine PDX 1000 amp wired to the rear. My guy took signal from the bose sub amp at the rear, drivers side of the vehicle.
This arrangement is working out damn good IMO.
I came from an Alpine D310 deck with phoenix gold 4ch amp, hertz front components and alpine rears, and subs on my old car. I felt the sound quality was really good.
This is right up there with what I had. The bass level for my deck is set to 0 and it pounds.
3) I also had a compustar pro installed. there IS a bypass kit that allows it. No you do not need an extra key. my Intelligent key still works except I now arm/disarm, lock/unlock, autostart with my compstar remote. Since I've had a compustar for the better part of the last decade this is no big deal to me.
4) Seeing as I'm in Canada and the market is a little more limited locally, I've contact AnzoUSA who makes the headlights for info on getting a set up here. I've read some people who bought headlights off ebay got ripped off or substituted so buyer beware.
I'm not a huge fan on the halo's and LED's. I want the headlights purely for the projectors so I can throw in HID's and be a little more public friendly.
If you want HID's be aware of the DRL system. From what I can tell it uses the highbeam on lower voltage.
I've been advised to get a Bi-halogen HID kit. (HID low beam, halogen high).
I'm waiting to see about the projectors before I do this because the projector set seems to split the high/low 9007 into 2 separate bulbs.