Anything's possible, but there is no official plan to do a second city loop re-configuration.
What John S described above, (through routing Clifton Hill to Ringwood via the loop) is one possibility - although whilst it definitely makes the network more legible (every line follows the identical path inbound or outbound) it doesn't free up additional capacity compared to leaving those two loops as-is.
One option I drew up some years ago is below (it's a variant of one of the previous iterations of the network development plan).
A reservation I have about the MM2 route, is that it only services two CBD stations, Southern Cross and Flagstaff, one of which is the lowest demand CBD station of all.
So I though why not split the MM2 proposal into two sectors, combined with a second city loop re-configuration.
The western half of MM2, Werribee-Newport-Fishermans Bend- Southern Cross, then gets through routed to Belgrave and Lilydale, taking over both the current Burnley and Clifton Hill Loop tunnels (shown below in blue).
Mernda runs via Parkville and Flagstaff before reaching the surface at Southern Cross then over the viaduct through routing to Glen Waverley and Alamein. (shown below in Red)
Hurstbridge through routes Flinders St - Southern Cross - North Melbourne then onto Newport (or alternatively you could send Hurstbridge to Upfield and leave Sandringham paired with Newport)
Hence no loops.
Parliament, Melbourne Central and Flagstaff have two reconfigured through routing lines.
One that swings via North Melbourne (the Frankston-Craigieburn line per current plan)
Another that swings via Southern Cross (the Werribee to -Belgrave and Lilydale line)
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