Why are you ok with a gold plated service for Dandenong and Frankston, but not Geelong?One needs to look at things on a case-by-case basis.
The sooner Melbourne has a Paris RER style express network the better. Bring the service up to standard, don't drag it down to the lowest denominator.
With Pakenham, the Latrobe Valley, Cranbourne/Clyde, and a connection to Frankston serving the greater Mornnington Peninsula and Western Port, an additional SG track pair to Dandenong is more than economically justified. It would be highly utilised, and combined with true, high capacity BG metro services would help develop both Dandenong and Frankston as principal suburban centres.
On the other hand, given the lack of sprawl to the west, operating Geelong services alongside Werribee services is the more feasible option in that case (with connection from Newport to SCS with two stations in Fishermans Bend). This could preferably be achieved through extension of Werribee services to Geelong (eg. with six stops b/w SCS and Werribee), or alternatively sacrificing capacity and reliability for reduced journey time by expressing Newport to Werribee on Geelong runs.
I'm not sure if you understand how the RER operates, since what I've described for Geelong is exactly how things would be done in Paris. The metro and RER routes run largely independent of each other, with the latter supplementing the former, rather than existing to exclusively serve the outer regions. The main difference being larger station spacing and rollingstock with more seating in the case of the RER.
The days of closing stations are over. Although some might have little use at the moment, it would be political suicide to do so. The whole point of this discussion is to provide an proper alternative to the freeway for commuters to Melbourne and Geelong. We want more people to live in Geelong, and to facilitate this, we need a decent express train to Melbourne. There is plenty of space beyond Newport on the Werribee line, other than perhaps in Werribee itself. Putting in an extra two tracks to accommodate trains at least every 10 minutes to Geelong is justifiable.
Geelong as an extended service via Werribee/Fishermans Bend is perfectly capable of achieving this, there is no need for express trackwork to skip three suburban stops (you haven't mentioned what happens after Newport, you would either need to extend those tracks all the way to the city at great expense, or end up with an unreliable mess as you try to converge everything down). Even as it is, most commuters to the CBD use the train - if one doesn't, their problem is with the journey from their home to the station, or the city to their workplace, it has little to do with the quality of the service between Geelong and the city.
The common denominator between SRL and the Geelong High Speed Rail projects is population. The government is seriously concerned about the great increase to Melbourne's population. SRL is designed to remove the unnecessary pressure on the CBD for cross-city journeys. Yes, it comes at a high price, but the consequence of not building it is a huge increase in congestion over the next few years. Similarly, High Speed Rail is one of many ploys to develop Geelong as a genuine second city in Victoria. While it will eventually likely be connected to Melbourne via suburbia, it has plenty of room to expand.
The SRL will do squat for reducing congestion, and the real consequence of such a polished turd is leaving nothing available to improve the suburban bus network, which is something that could actually achieve such results
Also, Geelong and Melbourne will thankfully never meet, due to the sewage works and airport.