Problems that I have noticed so far. I may also be wrong on some of the track layout. Only going off what others have told me.
Most Ballarat bound down trains will use the 'new' platform at Bacchus Marsh which is okay as it's straight in from SCS with no diversion.
Then going past Maddinley the Ballarat trains will have to slow to 80kph to get back onto the main line for the climb up the hill to Ballan.
Then before arriving into Ballan the service will have to slow to 80kph to divert into the new platform at Ballan. Depart and then stick to 80kph until the train leaves the loop on the down side of Ballan.
Increase back to 160kph to the former junction at Millbrook, cross the bridge then back to 80kph to divert into the 'new' loop replacing the Bungaree North line.
Stick to 80kph while crossing the UP pass if its running on time, then divert back onto the main at 80kph then increase back to 160 between the former junction at Torpys Rd before slamming the brakes back on for the 80kph speed limit down the Warrenheip bank.
Get through all the 40kph through the Ballarat yard, then after departing Ballarat stick to the new speed limit of 80kph to Wendouree which was 95kph.
Why the new loop at Millbrook through to Dunnstown couldn't have been duplicated as far as Warrenheip and then the Geelong line upgraded to concrete down the hill to Ballarat I have no answers. The Geelong track leads straight into platform 1 at Ballarat with no crossovers and won't delay a Melbourne service now using platform 2 all day.
It would have given them 19km of double track with little effort.
A dead end siding off the main at Wendouree is stupid. The second former down line Ballarat to Wendouree could have been reinstated with little work. It's all mostly there with only 1km removed. A poor mans solution to reinstate the pointwork at Doveton St (while we wait for SG to go through the area) would be straight forward the signals allow for it. A crossover could have been installed near Wendouree to allow Ararat trains to get from the down line to the Ararat platform at Wendouree.
Trains could go up and down from Wendouree to Ballarat with the only bottleneck between Lydiard and Doveton St.