The Y-U-S should be renamed the 1/Yellow line.
The B-D the 2/Green line.
Sheppard should be the 3/Purple, etc.
GO should letter their lines...
Lakeshore West should be the A/whatever colour they want
Milton should be B/whatever colour they want
Georgetown would be the C/whatever colour they want, etc.
That would be similar to Paris where the subways are numbered and the regional rails are lettered. Colours should be used as a secondary way to determine the line. The names we use now -- "Yonge-University-Spadina subway," "Georgetown corridor," etc. -- should be phased out as they are a mouthful anyway and not fully accurate.