The UP Express train is scheduled at 8 minutes to Union, the subway at 19 minutes. Switching trains at St. George is like 1 min at most, so 20 min total. Assuming the walk from the subway to UP Express is 3 minutes, the shortest time to get to Union via changing to UP Express is 11 minutes, the longest is 26 minutes (just missed a train and have to wait 15 minutes). On the subway the shortest time is 20 minutes, the longest is also 26 minutes (assuming maximum 6 minutes between Line 1 trains).
Also, it's possible the transfer with the new connection will be shorter than 3 minutes, so the times for UP Express might be less.
The two also arrive at different locations at Union Station, so the walk to your final destination will also make a difference.
Essentially, for certain trips it maybe be faster on average to take UP Express, not sure if it would be worth the cost.
Now once Kitchener GO line is more frequent, and if the fare integration stays the same, then the extra cost would only be $0.40. Though the Kitchener GO is currently scheduled at 12 minutes to get to Union, so that changes the calculation a bit.
So no clear winner IMHO.