1) Simply sending all "SmartTrack" trains to Scarborough Centre may be a workable solution. Regular GO trains (3 or 4 per hour) would continue to operate on the Uxbridge sub, serving Agincourt, Finch East, Milliken stations, as well as all stations in Markham.
At the same time, 4 "SmartTrack" trains per hour would serve Lawrence East Stn, and Scarborough Centre.
If large trains are used (AFAIK, a regular GO trains has capacity of about 2,000), then we would have 8,000 pphpd total capacity between STC and Kennedy. That's 50% more than today's SRT, and satisfies the latest demand estimate of 7,000 pphpd.
At Kennedy, some of the RER riders would alight and transfer to the BD subway or Eglinton LRT, leaving some room for more Union-bound riders boarding at Kennedy and at Main Stn.
But overall, that's not a perfect option: not much room for the further ridership growth, and large trains may not be optimal for service inside 416.
2) Option 2 is to add "Kennedy shuttles", running on the same rail tracks. The Uxbridge corridor is relatively wide between Kennedy Stn and Ellesmere, two pairs of tracks can fit there. In addition to 4 STC - Union trains and 3-4 Markham trains, we can have 4 or 8 smaller trains running between STC and Kennedy only.
The total capacity would depend on the train size; should be enough to handle the demand. For example if we have 4 Union trains per hour with capacity 1,500 each, and 8 shuttles with capacity 1,000, the total would be 14,000 pphpd.
3) Option 3 is same as Option 1, with an additional surface light rail line on Danforth / McCowan. The total capacity (STC to Kennedy) would be something like 11,000 pphpd (4 x 1,500 on RER, and about 5,000 on the surface light rail). Plus, that would provide a good list of choices for the riders. Those heading to the vicinity of Union, or even the Dundas West area, would wait for the RER train and get express ride. Riders transferring to BD subway or the Eglinton line, might opt for slower but more frequient McCowan LRT.
Now, although such solutions might be reasonably popular with the locals (if proposed), they require out-of-the-box thinking on the part of the Mayor's office and the TTC brass. Given that they didn't look at anything like that back in 2013 or 2015, I'm not very optimistic they will do so in 2018.