Why is 1000Base-T RJ-45 pinout scrambled instead of having each diff. pair in sequence ?
If you step back to the telephone days where RJ-11 was used, the center pair was used for 1 line, then you would step your way out (one side of the pair on each side of the existing line) for each additional phone line. This made things very nice for compatibility between like a 2 pin cord plugged into a 4 pin socket.

RJ-61 is similar to RJ-45 except that the pinout follows the same pattern that was used in RJ-11. The problem with this method is for high speed systems the outer set of pins are too far away from each other for proper noise rejection like you would hope for with twisted pair. Thus, the advent of RJ-45. Keeps some of the standards set in RJ-11, but also allows for higher speed data.

For what matters most to you will be the signals you are passing and the compatibility you would like to keep with stock cables. What I mean by this is that you can wire the connector however you want, but if down the road someone will try to use a stock Ethernet cable, or an extender cable, or something like that, the pin orientation might make a different if you are relying on the twisted pairs to reject noise.