3 way switch question

I think I'm loosing my mind, so I'll ask the question to the experts.
As some of you may remember, I'm building a house in Wisconsin, and I'm in the process of wiring it up (200A, 40 space SquareD panel, underground feeder). I currently have about 75% of the wiring done. I have a few 3 way swiches in the house, and for some reason I used 12-3 NM-B as the travelers. The power will go into the switch where the light is connected to. The more I think about it the more I think that 12-2 should have been enough. Do I need 12-3, or is 12-2 enough? I have 12 gauge wire throught the house (the whole house is now yellow ), with the exception of the high load items (AC, rannge, WH, dryer).
The plan I have is to run each bedroom on its own breaker (3X20A), each bathroom on it's own breaker (2X20A, GCFI breakers), LR outlets (20A breaker), lights in the living room, dining room, hallway, breakfast and kitchen on one 20A breaker, fridge on it's own 20A breaker, dishwasher+diskposal on a 20A breaker, 2X20A circuits for the 8 countertop outlets. I have 2 outlets in the breakfast nook, 4 outlets in the dining room and 2 outlets in a hallway. None will be used at all times, and probably the only load ever placed on them will be the vacuum cleaner. Should I run these on a 20A circuit? Can I connect them somewhere else? It would seem a wast to run a 20A circuit just for this load.
There will also be 2x20A circuits run to the garage. 1 circuit will supply the work bench outlets (no major tools), and one will supply the opener and lights. 1 light ran off a 3 way switch operated from the inside of the house/garage side door) will run off the 20A lighting circuit inside the house.
There will also be at least 6 outside lights, all single switch, controlled from 3 separate locations. Should I run them off a dedicated circuit, or can they share one? Most lights will be the outside wall lights, but 2 will probably be floodlights. I don't foresee any more then 800W of load due to those lights. Coupled with the at most 1200W load of the inside lights on the lights circuit it will only be 2000W (assuming I'll use 100W light bulbs, which is highly unlikely).
Of course, there will be a 20A circuit for the smoke detectors. Probably ACFI, I'll have to ask the inspector.
This is my first time using NM-B cable, I've always ran conduit before, so I dind't have to worry about grounding wires and protecting the cable. I know that if I go through a stud and have less then 1.5" of space (which is very difficult to have when drilling through a 2X4 interior stud) I have to use a metal place to protect the cable. Will the same apply if the cable is simply running up and down the stud?

 

Yes you need 12/3 between the 3way switches. You 2 wires for travelers and one for common + ground.

 

Code prohibits you from putting the hallway receptacles on the same circuit as dining room and nook receptacles.
I recommend (not required) one circuit for each.
1.25", not 1.5", measured from the edge of the hole to the edge of the stud. Not so difficult to do.