Depends on the rolling stock they purchase. Some trains like the Silverliners in Philadelphia have stepped access for low platforms and step free access for high floor stations.
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There is also the prospect of a dual level railcar, such as those KISS EMUs being ordered for CalTrain:
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Of course, if we didn't go with the dual platform option, I don't really see a huge problem with increasing platform heights across the network. Assuming it costs something like 20 million to do it at each station (and with many stations coming up for renovation, this might not even be an issue) there are ~70 stations in the network (Union station would be prohibitively more expensive), the extra costs associated with the addition are around 1.5 Billion dollars. Given that RER is supposed to cost some 20 Billion, 1.5 for decreasing dwell times by a factor of around 30-50%, in my eyes, is worth it. Even then, there are many stations (ie Guelph, Acton, St Catherines, the Bowmanville Extension, Bradford, Newmarket, Old Cummer, Langstaff, Centennial, Lincolnville) that won't need an entire 12-car high floor platform. Since these trains will likely be connected EMUs, the middle of the train could stop on a smaller platform that can accommodate 3-4 cars (Which is still a fairly long platform) at these lower ridership stations, bringing down costs.