Warning: this post is a little rambly, I was throwing thoughts onto the page as I went.
No reason why MM2 can't be 4 track. Two for express and two for stopping.
What this brings up is the problem with VicRail in its current state, the division between Metro and VLine. Needs to be split by stopping pattern and distance.
MM1 not starting at Caulfield is the biggest tragedy, because doing so would have allowed an express path for EXPRESS trains from Pakenham, Warragul (and beyond) and Frankston (and Stony point) from having a dedicated track into the city (Frankston via Dandenong), assuming Caulfield-Dandenong is quadded.
Again, Allow the Geelong line to be extended to Colac, Torquay, Drysdale and allow it to run express into the city, whilst allowing simultaneous stopping services alongside it. Untangle the Altona Loop and allow it to serve the south side of werribee. Express trains can connect at Newport and Lara for those who need to connect between.
This issue is because Melbourne has developed heavily east of the CBD. Ardeer still has a diesel service, and it's only 14.5km from the CBD as the crow flies, whilst Pakenham is 54km as the crow flies, and more so by track distance.
Werribee wasn't duplicated until the 60s and wasn't sparked beyond Newport until the 80s, and was a VLine service before that.
So Geelong isn't trying to have it's cake and eat it too, it is the easiest and busiest path to trial proper express services into the CBD, as it becomes arguably Melbourne's 2nd CBD. Pax from Belgrave wouldn't want an express service that went via Doncaster and Clifton Hill, which is the same as providing Geelong with an express path via Tarneit.
With the proper planning in place, there is ample room for Express services Box Hill, Dandenong, Frankston via Dandenong, Lara, Bacchus Marsh, Sunbury and Wallan into the city. No reason we can't start with Geelong.