Something of a fantasy map.
There are five major components to this.
1.) Yonge Extension: I went kind of over the top and imagined it extending all the way to Elgin Mills. A more realistic/practical goal would probably be the current YSE proposal. But an extension from a terminus at Hwy 7 could be accomplished cheaply using the nearby rail corridor and spacing stations way out.
2.) DRL: I've opted for a typical rail corridor DRL, though extended further into Agincourt & the Junction. In order to save costs, this DRL would poach rail corridor space from GO and in Union Station. If more money became available I'd rather have a Queen alignment, but I think this would be more economic. The only substantial difference would be my route skipping Flemingdon and cutting across to Eglinton/DonMills. This should lower construction costs and better facilitate regional trips, while Flemingdon would apparently have been quite low ridership anyways.
3.) Regional Branches: The only really novel part of my fantasy would be having GO/REX feeder routes branching off of my DRL. This isn't even that novel, actually. I know drum118 has suggested running the Richmond Hill line into the DRL and it's pretty common in Japan for commuter rail services to run through subways. This should kill two birds with one stone. It would be easy to transfer tracks currently used for GO to be used by the DRL and it would bring regional rail service to most of the 416/905. The exact service levels would depend. Assuming the central DRL trunk was built to accomodate 30-36 tph, during peak the western branches could see 10-12 tph each and the eastern branches 15-18. Those frequencies could allow even further branching (e.g. 4/10 Brampton trains serving Pearson, or a spur to the Buttonville development). To keep costs low and travel times high, station spacing would be on the order of every 3-4km.
4.) Reconfiguring GO: Transferring the busiest parts of GO to this new network would raise questions for the remainder of the GO Train network and regional rail in general. The fringes of Lakeshore West, Lakeshore East, Georgetown & Milton Lines wouldn't be served by this new network, nor would Barrie or Richmond Hill. These routes could be configured into a more proper regional or intercity rail or bus network. Some routes, like Richmond Hill, would probably just be converted to bus. Others though may, in future, become part of a Southern Ontario 'slow' HSR network using high speed DMUs, something like the Chicago Hub.
5.) Local Transit: My fantasy map didn't contain any kind of LRT or BRT system. I felt those systems weren't really relevant to illustrating the regional rail network I imagined, so I ignored things like the Finch West LRT or Scarborough LRT or Hurontario LRT. If a network like this ever got built, I'd expect most stations to connect with at least one high-volume surface route (either LRT, BRT or some kind of 'BRT lite'). I'd imagine that surface route investment would yield way higher cost benefit ratios than my rail network, so don't read their absence in my proposal as some kind of subways uber alles thing.
I'm not sure what the total cost of this network would be. It would require some tunneling (e.g. in East York), but proportionately little. Mostly surface running and infrequent station spacing should keep total station costs down. The cost of the regional branches would be related to what extent they reuse existing GO infrastructure. In total I'd guess between 15-20 billion? That's obviously a lot, but considering the Eglinton-Dundas West DRL would probably cost about 10b and REXifying some GO lines would probably cost a few billions it should be roughly cost neutral with current proposals.
I'd argue my concept is better because Toronto could avoid having to build an expensive tunnel across downtown, while our regional rail network would gain better access to micro destinations other than Union, increasing its usability.