Getting back to the core problem that the Metro is designed to solve...basically the need for two extra tracks through the CBD area, surely the lowest risk, quickest to build and cheapest solution to removing the networks biggest bottleneck is to expand the Flinders Street viaduct.
For those who know more about the finer issues of scheduling trains, why wouldn't simply expanding...or building a new viaduct between Flinders Street and Southern Cross with an additional track pair running into platforms 10 & 11 via the new platforms 15 & 16 at Southern Cross be an equally valid solution to the capacity problems? Platforms 15 & 16 for the Regional Rail Link could be replaced with two further platforms 17 & 18.
In terms of operations, this would allow the Sunbury (and future Melton lines) to run direct through to Frankston via platforms 8 & 9 and Laverton, Werribee and Williamstown to terminate at 10 & 11. Sandringham would still terminate at 13.
This would remove Sunbury from the Northern loop and Frankston from the Caulfield loop. Two huge bottlenecks removed there and no tunnels required.
It seems so obvious there MUST be a flaw in this plan. Oh and it also has the benefit of keeping the Pakenham and Cranbourne line trains in the full City Loop, which the Melbourne Rail Link would not and Frankston trains would also still run through Flinders Street...