I suspect that at least philosophically, nobody at the Commission would have any major objections to dhett's sensible proposal. But I do see three obstacles, one logistical, one regulatory and one philosophical.
Logistical: The FCC is already underfunded and understaffed, especially in the "un-sexy" Media Bureau. Allowing stations to use their RF channels as their major channel numbers, in the absence of conflict, requires a definition of what constitutes "conflict." Writing that regulation takes time and costs money, and enforcing it and resolving disputes takes more time and costs more money. Who's paying? (And what does constitute conflict?)
Regulatory: One of the big reasons broadcasters wanted to keep their analog channel numbers as their ATSC major channel numbers was cable must-carry. Cable systems are still required to carry must-carry stations on or below their major channel number, and to honor historical cable carriage positions. Dish and Direct use OTA major channel numbers almost exclusively. What happens in Boston when WMFP decides it wants to begin using "18.x" instead of "62.x" (a "no-conflict" situation) and then goes to Comcast, Dish and Direct and demands carriage on 18? Again, it's a situation that probably could be resolved - but who's paying for the staff to do that?
Philosophical: The UHF band is about to be repacked in the next few years. If I'm KASW, do I want to pour promotional energy and money into pushing "49.x" if I might be sent down to 25 or 36 or whatever come 2014? And who resolves the conflicts that might result from that round of repacking? Would stations be allowed to take their pick of either their old analog channel, their first-round ATSC channel or their repacked ATSC channel as a major channel number? Yet again - it could certainly be resolved, but by whom, and at what cost?