There will be some bugs to work out as Presto goes live on streetcars. Even Brad Ross is admitting they need to figure out how to deal with changing streetcars due to a short-turn.
Really, the best option is to allow 2-hour transfers, but the TTC is afraid of the up to $20 million they expect to lose in fare revenue. And don't expect John Tory's administration to make up the difference; it's still too focused on cost cutting (at least everywhere except the police).
I wrote about the problem (and the solution) on my blog on Friday.
http://seanmarshall.ca/2015/12/04/its-time-for-two-hour-transfers-on-the-ttc/