I agree, a tracked format can be much better done. I've really noticed after using ones like Raster Music Tracker and Goat Tracker, though the soundchip capabilities are different, the methods used would adapt well to the NES.
Something as simple as the envelopes used with MCK make a huge difference. The programs I mentioned above show ways that this can be adapted to a tracked format.
If this new tracker program could import NED files (but not export), I think that would be the best way to continue what NT2 had started.
I can't be much help on the PC side with developing it (other than maybe testing, heheh), but I would totally like to help out with the format design and NES replay code if any help is wanted.