The biggest issue with the subway extension IMO is that it assumes all TTC users from Scarborough want to get downtown. Thus, unless your destination falls close to the one subway station between the end of beginning of the line, there's no service other than buses for any trips within Scarborough.
The assumption led by many outside politicians that Scarborough commuters only want to travel short distances was the biggest issue that set the City back. We can finally move on with a plan that opens up the options and supports various important criteria in creating an overall network for this massive area.
And really the exact same assumption you have could be said for the RT but with the subway the stations will now be far less isolated, in more central locations for the feeders, not to mention far better connectivity for not only the commuters but the for future of growth in the Centre. Its a far superior line.
The subway addresses the various glaring flaws from the RT and will be one of the most integral parts of the 'network' in Scarborough. The Durham-Scarborough BRT, EELRT, RER will all be part of an overdue upgrade for multiple forms of travel in the next decade. This will change the current travel patterns quite a bit. The Sheppard subway and hopefully more BRT lines will gain traction in the following decade as required to continue to improve flow thru the entire network