As a regular 25/29 rider, I can attest that the ridership is often pretty lopsided and there's a number of problems with it that make it a poor substitute for rail service and a poor connection to Toronto. A lot of the service expansion (and corresponding ridership growth) of the last 5 years has been with express versions of the 25 like the 25C that goes directly from the Waterloo universities to Square One. This is great for students going home on the weekend to Mississauga, but a poor service for pretty much any other situation - most of the population is in Kitchener, which is only served by the milk run 25, while only northern Cambridge gets GO service, with none in Galt.
The 25 is very poorly integrated with local transit (not entirely GO's fault by any means) and its stops favour the highway-oriented park and ride system rather than local transit terminals or light rail stations. For example, it bypasses Fairway Station in the south end of Kitchener which is one of the most significant hubs in the GRT system, and instead has an on street stop on King in a pretty desolate area and a stop at the Sportsworld park and ride instead. The 25 anecdotally can also get very delayed passing through downtown Kitchener, which can affect people's ability to make transfers, and add to the dubiousness of travelling on it if other options are available.
The problem with this kind of service model is that it becomes a self-fulfilling prophecy and the south end of the region is a dead zone for intercity transit of any kind. Improved GO train service is breath of fresh air because it allows a direct connection to Toronto, as well as to actual nearby cities (as opposed to the bustling metropolis of Aberfoyle, where the 25 passes through), and the Kitchener railway station has decent integration with local transit which will only improve over time.
Realistically, I think a number of temporary improvements could be made: perhaps a rationalization of all these Kitchener line bus-to-train routes in Kitchener, Guelph, Georgetown, etc so you still had the peak direction commuter express going direct to Bramalea, but off-peak have a real Kitchener line bus making all the Kitchener line station stops. The business case identifies that Kitchener-Guelph is a big untapped market for example, and that's not an easy trip to make by bus with the transfer at Aberfoyle. It would also help with phasing in rail service. It couldn't compete with the express 25s for the student market in Waterloo, but it would help create more options for people in Kitchener, and would be a worthwhile alternative to just increasing the frequency of the 25, especially since so much of the 25's travel time is spent getting on and off the highway around Kitchener and Cambridge.