Hm, I don't know if Jigsy's post is only visible to me, but just by going on the scenarios outlined both by the OP and Spitfire in his own suggestion, the Window > Order option does precisely this.
I too like my channels in a certain order and that option has served me well so far!
That's not to say this shouldn't be implemented, but I'm just pointing out that your specific problems can be resolved with current features.
Regards,
