Circuit #1 (new 20A)
1 - run a new 20A circuit from panel through crawl space, up the
invisible room chute into attic
2 - take this cable over to master bath outlet #1 (new GFI)
3 - take the outgoing load from this GFI outlet to master bath outlet
#2
4 - take the outgoing load from this outlet to 2nd bath outlet
Now Circuit #1 is 20A, 12 AWG and has just three outlets on it, all
GFI protected. *As mentioned above I'd have to do something with the 2
downstairs outlets that used to be on this circuit.

I might be wrong, but I beleive each seperate bathroom must be on its
own 20A circuit.

Circuit #2 (old 15A)
1 - this currently comes from the panel into the attic and runs to the
master bath outlet. *Since I'm wiring these outlets with the new
circuit #1 above, I cut this line and route it to handle the bathroom
light switch, vanity light, and light/fan FOR BOTH UPSTAIRS
BATHROOMS. *There will be no heater, which I've read means that I can
use 15A. *Some have told me the light/fan needs to be GFI and some
have told me it does not - if it does need to be please tell me the
section of code specifically from NEC. *If it needs to be GFI I'm
tempted to put in a GFI breaker instead of messing with mixing the
light fixtures and routing them into Circuit #1.

This sounds good, leave the 15A to feed some lighting and fan, plus
the 1/2 bath and outside outlet. This means you don't have to go crazy
re-routing new wires downstairs.
As I've said, if the fan/light is inside the shower/tub area it must
be on GFI. Outside of it, it does not need it.

Circuit #3 (the other old 15A)
1 - this currently comes from the panel into the attic and powers the
whole side of my house (master bedroom, master bath fixtures, 2nd bath
fixtures, 2 closets). *Since the bathroom fixtures will be taken care
of by rerouting Circuit #2 above, this circuit will basically just
power my bedroom and closet lights now.

I don't see a problem with this.