RER's initial service plan is to have hourly express (first stop is Oakville) diesel service to Hamilton throughout the day, but mid day 15 minute service will make all stops. The hourly express service will be nice for those on the further ends of the line, if you can time your trips around the schedule.
I've also seen RER saying first stop of diesel express to Hamilton is Burlington.
Basically electrified RER is allstop to Burlington, and diesel RER is express to Burlington and allstop afterwards. If it takes the West Harbour route, then potentially it could be hourly to StCat. To make commute time feasible, it would have to be literally express to Burlington.
That's what I saw in the RER business case.
All subject to change, of course.
Metrolinx 2041 RTP proposes 15-min allstop RER to downtown Hamilton. This was emphasized -- Metrolinx intends eventual 15-min electric service to Hamilton "after 2025" (meaning time range 2025-2041). That was said by them when I went to a Hamilton consulation at the Hamilton Public Library, which was very well organized by Metrolinx employees, including assistive services for the deaf (I am a deafie) including closed captioning.
Now....
Knowing Niagara GO is being worked on. Based on further speculation based on Niagara GO plans and Metrolinx 2041 RTP, it could then be hourly diesel (or dualmode) RER to St. Catharines (plus Niagara Falls during peak, using guaranteed liftbridge slots). To keep that practical commute times, you literally need express to Burlington, just like what it already says in the RER Business Plan. This isn't mentioned in the 2041 RTP, but it makes a hell lot of sense. Send the frequent electrics as a downtown-to-downtown service, and send the hourly diesels to St. Catharines.
CN/CP may resist electrification for now, but maybe not by 2030s. Legislation changes (climate change subsidies/tax benefits creating new electrification carrots for CN/CP) may allow them to reluctantly permit one or two tracks per their corridor to be electrified as a compromise. New road bridges over CN/CP corridors are already being raised to meet GO's minimum electrification heights for electric-locomotive-pulled Bombardier BiLevels -- that's what happened to Hamilton's still-relatively-new John Street bridge. Eventually, barriers against electrifying via CN/CP corridors, will slowly be removed. Not this generation probably, but by 2041.
That said, Niagara route is unlikely to be electrified simultaneously by 2041 unless an Empire Corridor electrification initiative happening (electrified "Acela Express" style service Toronto-NYC) under a future U.S. administration.
In theory, that ties in well with Niagara RER and a Welland Bridge grade separation (2041? 2051?) -- to enable a Toronto high speed link to the states -- while simultaneously bringing electrified RER service to Niagara Falls (when ridership warrants).
The Welland Canal grade separation isn't worth it just for RER only, but if you combine Niagara RER + high speed to USA, then the economics of the grade separation may then make sense (under possible 2041 ridership, at least).
For now I think Metrolinx could bring 15-min allday to Hamilton and hourly diesels to StCat by 2041 (Niagara Falls during peak)