Here is a revised version of a fantasy map I put out a couple months ago. The naming scheme is mostly arbitrary, but A Lines go through Metro Tunnels, B Lines are Cross-city, C lines are City Loop and D Lines are Diesel.

All the lines are separate enough so that 10 minutes to everywhere is possible, and done all day. In peak hours, all lines run at 5-7 minutes, with closer stations at a 2.5 - 3.5 minute frequency. CBTC allows for 2.5, normal signaling would be upgraded to allow for 3.5 minutes.

All A lines would use HCMTs, other lines would use X'Trap 2.0s, and the remains of older generations.

Here's the breakdown, clockwise around the bay.

B1 Line:

The Williamstown line runs direct to Sandringham via Flinders Street. Williamstown and Sandringham stations would be rebuilt with two platforms, possible with a third or fourth track in the middle for stabling.

A2 Line:

The Werribee line runs via a second Tunnel. The Altona Loop would be separated, and extended down to Point Cook, running elevated down the middle of Central Ave, and Pt Cook Rd. A stabling facility would be built south of Pt Cook Homestead Rd.

MM2 would remove Rushall Station, and rebuild Merri Station in trench style, allowing for LXRP of Clark St. A track connection at each end of the Tunnel would be kept for operational flexibility and services running while MM2 is under construction. A new station would be built at Black Forest Rd for interchanges with Geelong and A3 line services.

The Mernda line is extended to Whittlesea, and a branch is constructed to Wollert. Epping station is renamed East Epping station. Lalor is rebuilt with three platforms, and a flyover is built that leads into the elevated section over High St.

A3 Line:

The Melton and Wyndham Vale lines would be electrified, feeding into a new pair of platforms at Sunshine, and along to West Footscray. New stations would be built along the corridor to service new growth. Due to space constraints, the line would enter a tunnel after West Footscray, with new platforms underground at Footscray, creating a paid underground concourse.

The line would then run to a new station at Docklands, East Melbourne, near Fitzroy Gardens, and North Burnley, somewhere on Burnley St. New underground platforms at Burney Station, and a massive rebuild, and the Tunnel would end with a rebuilt Heyington Station.

The Glen Waverley line would be extended to Ferntree Gully, with underground sections just past Glen Waverley and Knox City. Ferntree Gully Station would be rebuilt as an elevated, 4 platform station, with the centre two platforms for terminating trains from Ringwood. The line would be duplicated to Upper Ferntree Gully, where some peak hour trains would terminate.

A1 Line:

The current Metro Tunnel line. The Sunbury line would be extended to Gisborne, and the Airport line would link in with a flyover near Albion. The Cranbourne line would be extended with a new elevated station at Cranbourne, and three new stations beyond, and a new stabling facility near Clyde. The Pakenham-Cranbourne junction would be rebuilt as a flyover, with 4 tracks into a rebuilt Dandenong Station, with 5 platforms, providing cross platform interchanges.

M1 Line:

A mostly underground Metro line, with interchanges at various stations. The line would run above ground, roughly following the Maribyrnong River and Steele Creek, beyond Flemington. The line would terminate with a Depot near Templestowe.

B2 Line:

A product of the City Loop Reconfiguration. The Frankston line would be electrified and duplicated to Baxter. A new station, technically closer to Roxburgh Park, but named Somerton, on Patullos Ln, elevated allowing the Lane to pass underneath.

Craigieburn station would be rebuilt with four platforms and a new concourse. The westernmost two platforms would serve the B2 Line, allowing for easy and direct stabling into the Craigieburn Depot.

B3 Line:

The Upfield line would be extended and duplicated to Wallan, with all former Vline stations being rebuilt to comply with LXRP. A fourth track is built between Burnley and Camberwell, and B3 trains run express along the outer two tracks of the section. Camberwell is rebuilt with four platforms. Burnley Junction is rationalised, but A3 trains can still connect to the B3 line if needed.

The Alamein line is extended underground to several new stations. The line is at ground level at Oakleigh, using the two former platforms, and then runs to SRL Monash, before surfacing at Mulgrave, just west of the Monash Freeway. The line then runs elevated to the north of Wellington Rd, crossing over and terminating near Napoleon Rd, with a stabling yard for terminating trains.

C2 Line:

The former Hurstbridge line is largely untouched. Macleod station is rebuilt to allow for better terminating peak hour trains. Clifton Hill Junction is not frequently used, and is rebuilt to allow for higher speed running, whilst still retaining the capability to service A2 line trains. Duplication is continuous to Eltham, with a second trestle bridge constructed over Diamond Creek.

C1 Line:

The Lilydale line is completely duplicated, with a new station between Mooroolbark and Lilydale, at Hull Rd. The former Belgrave line terminates at Ferntree Gully, connection with the A3 line. The line is triplicated from Camberwell to Blackburn.

SRL:

SRL is extended from Southland to Sandringham, connecting to a rebuilt Sandringham Station. The line is mostly according to current proposals.

D1 Lines:

Trains run from Baxter along a restored Mornington line, and along the Stony Point line. Several passing loops are built to allow for improved frequencies, and Vlocitiys are used, to improve maintenance simplicity.