Opinions are like fingers, and I'm going to offer you a handfull right now.
My first point is to forget 'code rules' or 'saving money' as your primary consideration. Rather, let 'good design' guide you. Doing so willhelp you avoid any code quagmires, and any changes you might have to make will be easier to make.
The short form of the 2011 is that if it doesn't have to be on a GFCI, it ought to be on an AFCI. Yes, there are exceptions - you can argue for the fridge and the stairway receptacles as examples - but, for all practical matters, that's the situation. You're not going to be running a dedicated circuit for the bath fan just to keep it off an AFCI, are you?
There are other major changes in the 2011 code, that will directly affect the way you wire a house. The effect is that it strongly discourages the use of either 'skinny' breakers, or shared neutrals.
In the past, it was common for one circuit to serve receptacles on both sides of a common wall. I suggest that you plan to use more wire, and have circuits organized by rooms, rather than walls.
With the increased number of circuits in today's homes, I suggest you plan on several sub-panels. One for each floor, the kitchen, and the mechanicals is a good way to start. The 'required' circuits have a way of really adding up.
According to the 'experts,' there is no reason not to add a GFI receptacle to an AFCI-protected circuit. I am not aware of any breaker that provided both protections.
Lighting circuits have become quite complex, with sundry dimmers, timers, motion sensors, electronic ballasts, and who can guess what else. I reccomend breaking the lighting circuits up - again - by area, and not having very many fixtures and devices on each one. Complaints of AFCI problems seem to turn up most common on these circuits, and they're the devil to troubleshoot.
Another suggestion is to wire the lights with 12/2, and the smoke alarms with 14/3. This will help keep you from hanging a light on the smoke circuit, and vise-versa. Bring your neutrals into the switch boxes, rather than splitting out a 'switch leg' from one of the ceiling cans - again, think 'troubleshooting.'
