I recall that the Stouffville schedule used to show trains stopping at Danforth - can't remember about Scarborough.
I can understand under the current timetable, that they may want to avoid stopping there, particularly now they can stop at Kennedy.
But I hope that they do start stopping again if they start running Stouffville off-peak or weekend service - as then train overcrowding is a non-issue - and it provides much needed extra service to the inner-city stations.
An increase in overall frequency would also negate this problem. The issue is too many people crowding onto too few trains. If people have more options, having to use a Stouffville train wouldn't have been as big of an issue.