The problem is multifold - ridiculous oversizing of certain stations (407, 2 busbays at Pioneer?!), poor finishes/workmanship (the concrete work at York U)
AoD
The problem with the TYSSE was that 2 stations were built for future developments: 407 for Vaughan developments and the 407 transitway, and Downsview Park for RER.
I've made this argument before elsewhere, but given the longer time associated with waiting for GO Transit (whether it be a bus or a train), the extra space is necessary. Prior to the COVID 19 pandemic, 407 was seeing a crap ton of York University students waiting in the bus terminal during the evening, to the point in which it was pretty much standing room only throughout the terminal. That terminal really needs to see better 25F service, and new services from Guelph. It has so much potential from a GO connectability perspective.
Downsview Park will be empty for the forseeable future, but when you consider the fact that they pretty much built an interchange station, the price becomes easier to eat (even though it's grossly oversized for RER)
Finch West was a good size given the fire code allowances, but the ceilings could have definitely been lower. Same with Pioneer Village. The 2 bus terminals is fine since they have to separate the fare zones, and since all the bays are in use (It's basically the finch station of the Spadina Line, or at least it will be once ridership and development along the line increases).
The only station I'd say is vastly oversized outside of Downsview Park is VMC. That station really did not need that additional bus terminal, but at least it wasn't paid for by the TTC.