I think you’ll find that the next new cross-river tunnel we’ll need isn’t for the South so much as the West. See the Inner City Rail Capacity Study from the mid-2000s, or the Minerva Plan. It’s sometimes referred to as the Clevewich line on here.
In the West, today we run about 17tph in AM peak (give or take a tph) out of 20tph available. With the vast growth around Ripley and also further west there’s plenty of demand yet to grow, as well as from more infill closer to the city. We should go to 24tph with signal upgrades, but still. Short term, CRR1 taking traffic off the Merivale opens up the possibility of e.g. Corinda starters sharing platforms with Cleveland trains but long term another track pair is needed.
We already have four tracks Milton to Corinda so we probably want to start the tunnel at ~Milton. Since the tunnel enters the city from the west, the logical place for it to go is east. This lets us serve New Farm and Hawthorne along the way before joining the Cleveland line somewhere near Cannon Hill. (Optionally, add a new branch SE to Capalaba.)
I don’t have strong opinions as to how the western lines split the tunnel and the surface; given Ripley’s pretty far out maybe the Springfield-Ripley branch goes full time express with all-stoppers to ~Redbank. This might require modifications to the junction layout though.
Why not the Northside? Well, the capacity upgrade the Northside needs isn’t a new cross river tunnel per se, but rather NWTC, Chermside, or else an in-place amplification along the existing corridor (6 tracks to EJ and 4 tracks to Petrie). It already has three sectors, it’s just that the boundaries are in the wrong spot; 2/3rds of a sector’s capacity used only by Ferny Grove post-CRR1.
With this amplification, we’d run FG/Airport/Doomben on the subs, Shorncliffe and Redcliffe on the mains, Caboolture and Sunshine Coast via CRR.
The Clevewich line means even less traffic on the Merivale bridge, just Morningside, Norman Park & Coorparoo really. As Southside demand grows with population and the Beaudesert line, it becomes very obvious that some Southside trains should start taking the Merivale Bridge again.
This requires quad-tracking to the sector boundary (or to Kuraby given LGCFR). Regrettably this necessitates another corridor rebuild along the Beenleigh line. I’d suggest picking a layout and sticking with it: centre express tracks to match the CRR portal, then with 2 side platforms given width constraints.
That leaves Gold Coast and Beaudesert via CRR, Beenleigh and Cannon Hill via the Merivale bridge. Salisbury should have a full flying junction of course.