Personally what I would like to see:
BM. This is the spec most reliant on pet damage and control. As it stands right now this is already the more 'unique' spec of the three.
Combine SV and Marks. This is a ranged damage spec. Keep explosive shot for a rolling tick. Keep the strong AoE. Keep Chimera shot as a minor method of self healing and marginally strong shot to the point that it's used in rotation. Aimed shot and/or LnL procs and all that would have to be played with to find a good balance between not being OP, playing smooth, and not having way too much going on. Obviously keep all the utility shots such as scatter, tranq, etc.
Some sort of melee based spec. Hunters don't HAVE to be all about bows and guns. Surely daggers and axes fit in to the theme of a Hunter just fine.
This would be the hardest to create from scratch at this point in the game, the most difficult part being making it unique enough to stand out from rogues, monks, and enhancement shamans. Ideally this would be the class that brings the raid cooldowns and utility, something Hunters can currently do but sort of in a crappy designed way with the entire "fill in the holes" approach to pet abilities.
Clearly my idea has a lot of holes and uncertainties in it at this time, but ideally something along those lines is what I would LOVE to see for Hunters in the future. A strong pet spec, a strong ranged spec, and a strong melee and utility spec. Right now the differences are really quite limited, and yes even at a top HC progression level. The biggest differences right now only come from the amount of damage signature abilities are doing. The play style remains almost entirely unchanged.