I also spoke with someone from Metrolinx yesterday at the Big Move Roundtable, specifically about Eglinton East and the possibility of elevating it. He made it quite clear without explicitly saying so that he thinks that that would be the best solution, but that there are a lot of political pressures to not make any significant changes. He said that there have been a lot of 'serious internal discussions' about what to do with that section.
So basically, the only reason why it's being built at-grade now is because of political pressures. Which is definitely unfortunate, because I can say with confidence now that if Metrolinx could have their way, Eglinton would be a 100% grade-separated line with an elevated eastern section.
Hopefully they will find some way to get the changes they want, even despite the political will to not change it. Maybe some back room discussions can lead to something. But it's good to know that they were thinking along the same lines that I am.