Okay, I've had a read of a few of the articles, and it seems that there is electrification to Wyndham Vale and Melton on the table, as well as obviously the airport line and the Geelong and Ballarat upgrades. I think the article in The Age suggested some of these could have been done via a tunnel between the city and Sunshine. Two thoughts:
One, it's a shame that Metro 1 had been scaled back to only South Kensington to South Yarra. I don't know if Sunshine was ever going to be part of it, but Caulfield was, and, yes, increased costs... but with all the tunnelling equipment already there and ready to go it couldn't have costed that much more, especially if they made it express to Sunshine with some sort of all stations service maintained. It would have certainly been cheaper than building an entirely new tunnel.
Two, I have mentioned this on other threads, but I believe Metro 2 is the answer to the West's woes; at least partially. If you get Geelong out of the mix, running the more direct route via Newport on new dedicated tracks (there should be plenty of room) and improving travel time and operational costs, then you could extend the Werribee Line onto RRL and have it terminate at Deer Park with seamless interchange onto relevant services. There is no point of expanding City-Sunshine even more, not now at least. Perhaps a direct tunnel/skyrail from the airport to the city would work, but the costs would be too great. I suggest that for the medium term, run services via Sunshine into Metro 1, then in future years allow V/Lines to use that line via the airport out to Bendigo and Seymour, freeing up space on the overcrowded Craigieburn and Sunbury lines. And of course along with that build the direct link. Bendigo and Seymour could then run via the freight tracks or in a new link from Albion to the city.
I should probably stop dreaming...