A couple of items to note, rolling stock wise:
1) Dandenong - Pakenham line upgrade was an unsolicited bid from MTM, but not the next generation rolling stock. Comeng life expiry starts in 2016-2017 based on date of entry to service and a standard 35-40 year life span of rolling stock unless a proper life extension is conducted. So the options would be to:
a) replace Comeng rolling stock completely with new fleet, and;
b) life-extend Comeng to provide short term coverage.
I would imagine that the Department of Transport and its successors would have been working on some sort of project to bring new fleet to Melbourne, a la VLocities.
2) Bombardier have existing Australian contracts with Victoria and South Australia, but it doesn't mean that they are the only suppliers in the Australian market, limited as it is. EDI Downer, with CSR Changchun, brought the Waratahs to Sydney. While Bombardier would have an advantage in having existing rolling stock designs and existing contracts, it wouldn't be automatic to say that they will get it. It was just expedient to extend the VLocity contract to provide new rolling stock, in the same manner as extending the Alstom X'Trapolis contract.
3) As a slight extension to the above situation with EDI Downer and the Waratah Fleet, this project has significantly gone over budget by a few billion dollars, at last examinen. I don't know if the procurement of Melbourne's latest fleet additions to the tram network or the rail network have gone over budget, but there are inherent risks whether one decides to build locally or internationally. The key is the contractual position taken by the vendor and purchaser, and also the checks and balances throughout the process to ensure procurement proceeds as smoothly as possible.
4) I would imagine that rolling stock design would be something that would take a little longer than just taking something off the shelf. The Comeng replacement requirement would be at least 1:1 of existing fleet, if not more. The original Comeng fleet was 95.5 six-car sets, now down to something like 93 after accidents and write offs. I would imagine that, moving forward, you'd want more than that number of six-car sets. Further to this, I would imagine that, while it would be fantastic to go to a HK metro style seating arrangement for crush load numbers, it would be unpalatable for commuters travelling in from Sunbury or Pakenham! I would hesitate to guess, given the Siemens and X'Trapolis fleet are 2 x 2 seating, that this would be the way forward.
5) Nine car trainsets are a great idea if the existing infrastructure could readily support such an extension. I believe that would be some major constraints at some stations on the network, including just on the Pakenham and Cranbourne Lines, that would create more hassle than its worth.
6) An item of note that benefits future procurement of rolling stock is that it appears that, moving forward, that Victoria will follow a UK Transport for London model. The state body does the main work in developing the scope of the project and outline, the operator and supplier deliver in conjunction with each other (well something like that). That's not necessarily a bad structure for procurement. TfL are proceeding with a massive order for Thameslink and a slightly less massive order for CrossRail using a similar methodology.
Just some thoughts. Consider also that Auckland have procured CAF rolling stock for their electrification, and Wellington have procured Hyundai/Rotem rolling stock to replace their 50+ year old fleet. Beyond Bombardier, Alstom, Siemens, EDI Downer and UGL Rail there are a lot of potential suppliers out there.
Coupled to this is the desire to provide a form of in-cab signalling or tech similar to ETCS/ERTMS/CTBC for Dandenong/Pakenham, and suppliers would seek to enable a seamless integration between rolling stock (existing and new), lineside infrastructure, and rail operations. The potential scope for the project could easily dwarf the amount of money currently assigned to it.