Oh yeah, the whole thing of trains running every 3-5 minutes and accepting TTC fares is never going to happen, and the SmartTrack branding will never appear on trains or in stations. I don't think anyone except Mayor Tory is deluded enough to believe that anymore, and I hope even he realizes it won't happen.
All SmartTrack is is John Tory riding Metrolinx's coattails so that he gets to take credit for GO RER, which was going to happen regardless. One or two additional stations in Toronto will be built which wouldn't have been, e.g. Lawrence East (which shouldn't be built since there should be an LRT there...) but that's it. Spadina-Front was going to be built anyways, as were Liberty Village, Mt Dennis, Caledonia, and Downsview Park; Lansdowne was a capitulation to local outrage over the Davenport Diamond and had nothing to do with ST. At least two of the four stouffville stations (east harbour/unilever and one of the other ones) would probably have been built anyways, he can take credit for Lawrence E and another one. The trains will run every 15 minutes, they'll be GO trains with GO livery with GO fares and the TTC transfer discount until such a time as region-wide fare integration is implemented, and at that point it's anyone's guess what fares will look like, but I promise it won't be a $3.00 (plus occasional $0.05-10 increases) flat rate.