The only routes that can support two tier services with current infrastructure are:
Frankston, Ringwood, Werribee
On the Frankston Line:
Tier 1: This would be Limited Stop via city loop eg South Yarra - Caulfield - Moorabbin then all stops.
Tier 2: Stopping all stations Direct from Flinders street to Moorabbin.
On the Ringwood line:
Tier 1: Limited Stop via city loop eg Richmond - camberwell - box hill then all stations to Ringwood. Every second train to Belgrave or lilydale.
Tier 2: Stopping all stations Direct from flinders street to box hill.
On the werribee line:
Tier 1: Limited stop via city loop eg North Melb - Footscray then all stops newport then Newport - laverton express then all stops werribee.
Tier 2: Stopping all stations to Laverton via altona Direct from flinders street.
Willamstown (Change Newport), Alamain (Change Camberwell) Cranbourne (Change Dandenong) would operate as full time shuttle services even during peak hours using 3 car sets.
All other lines would operate full time as stopping all stations.
All Gippsland vline would terminate at Dandenong and return to Gippsland expect Bairnsdale trains. All passenger would have to changed onto a metro train at Dandenong untill a 4 track line is completed.
All Bendigo, Ballarat Vline trains would terminate at sunshine with passengers transferring to metro trains at sunshine. The vline trains would terminate on temporary timber platforms north of the station and passengers connect via covered walkways to the metro trains untill the new regional fast rail tracks are completed.
Geelong trains would follow the werribee limited stop trains into Melbourne on the same timetable if need be due to limited passing locations between north melb and werribee. A faster geelong timetable would return upon the new line to sunshine being completed.
All the existing metro trains would have the seating changed to longitudinal seating for maximum capacity.
During peak periods the headways should be close to or better than every 5 mins and off peak/weekend no less than every 10 mins through out the metro system.
This is what would be needed to be done to get the maximum out of the current infrastructure that melbournes metro system has and probably makes use of every train at peak times (100% train utilization at peak)
Do the train servicing overnight/weekend so the maximum amount of trains are running at peak times.
Regarding faults on trains a peaks if the train can still move and stop it can remain in service with the faults untill the end of peak just to keep the system moving. After peak the train goes for urgent servicing. If passengers feel unhappy with the faulty train take the next one.
All cargo trains would be limited to Weekends and between 9pm and 5am Monday to Friday. To keep the system free for metro trains.
This is what needs to be done to handle any short term future growth on the system in melbourne. Longer term 3rd and 4th tracks need to build on any route with express trains and vline services to allow fast trips to return.