There's a million different set-ups. I've changed my system countless times and I'm still changing it.
It's basically going to come down too how much you want to change your center console. What I'm going to tell you next will be more than what BrianK is going to charge so just keep that in mind as well.
I'd personally take all the stock ones out and tap into the existing wiring, build baffles, buy or build a sub box, and stick an amp behind the passenger seat. At this point you have the basis to a personalized system. Now to figure out what source you want the brain to be. You have a few options like you mentioned. I'd go with the tablet to sound processor or tablet to bluetooth to sound processor. There's really no need for a headunit anymore in my opinion. This is the line output driver I use. I originally had my Iphone plugged directly in from the headphone jack but it sounded not good so I added this unit and it was a night and day difference.
http://www.amazon.com/Clarion-EQS74...354005815&sr=8-16&keywords=line+output+driver
Depending on how far you'll go with the center console there's a few ways you can do things...