I think it's about time this happened, the number and colour would be good identifiers, and would help avoid so much of the political issues around subways and LRTs, and what their line names are. When we want to build a new line, the working name could simply be "Line 6" or whatever, we could chose a sensible route, and then figure out the technology, whether it be subway, LRT, BRT whatever.
I would hope though that they add a letter as well, such as M1, M2, M3 etc (M being for metro). That way they could distinguish from GO lines, that would use a different letter and number, and maybe streetcars, or other rapid transit lines in the GTA.