$3 Billion would not get you anywhere near subway-like frequencies on an RER branch to STC. The upgrades necessary to enable that would be staggering. Rail corridors would need to be widened, grade separations would be necessary to eliminate conflict in train movements, Union Station would need to be massively reconfigured, likely with a tunnel running beneath it, signalling systems would probably need to be changed. This particular branch would probably need a new fleet of trains, more similar in size and design to the Toronto Rockets than the current GO fleet, because long, commuter-style trains aren't well suited for frequent subway-like service (because it takes them a significant amount of time to switch tracks).
I hate to poo poo the idea, but it's simply not realistic. We probably aren't ever going to see subway-like RER frequencies until we have an RER tunnel running through Downtown, in addition to a myriad of other auxiliary network upgrades.