I do agree that it was shortsighted to not include more platforms (underground) but not for a Subway DRL, for the expanding GO network. GO already takes up, what, 80% of the available platform space at Union? If we could move a majority of that underground at the expense of perhaps a lower ceilinged new concourse would work wonders for the station. Instead we had a retail focused improvement plan that did little to increase capacity (to my knowledge) of it.
The capacity constraints are due to the trains themselves, not the station. Those bi-levels take forever to load and unload, which is why the station feels more full than it actually is. And given the frequency (or lack theirof), you get a mad rush every time a train pops up as 'arrived' because people know it'll be an hour before the next one comes.
Smaller, more flow-efficient trains that run much shorter headways will go a long way to improving the flow at Union.
I envision that platform layout working like this (note, these do not correspond to the current platform numbers. In these numbers, each platform is physically a separate island):
1: Lakeshore westbound exit platform
2: Lakeshore westbound entrance platform
3: Lakeshore eastbound entrance platform
4: Lakeshore westbound exit platform
5: Milton-Stouffville westbound exit platform
6: Milton-Stouffville westbound entrance platform
7: Milton-Stouffville eastbound entrance platform
8: Milton-Stouffville eastbound exit platform
9: Georgetown-Richmond Hill westbound exit platform
10: Georgetown-Richmond Hill westbound entrance platform
11: Georgetown-Richmond Hill eastbound entrance platform
12: Georgetown-Richmond Hill eastbound exit platform
13: Barrie exit platform
14: Barrie entrance platform
Note that there is a standard here: enter on the left side of the train, exit on the right side. The enter and exit platforms would also be physically separate platforms, so the stairs up and down would be one-ways. Achieving a good passenger flow isn't impossible to do, you just have to segregate the movements of people accordingly.
Also, by having consistent platforms for each of the trains, people wouldn't need to wait in the concourse for their train, they would automatically know which platform they had to go to. And because the frequency would be much higher, they wouldn't be waiting very long on the platform either.
EDIT: Re-thinking about it, I suppose the exit platforms could be shared platforms (ie platforms 4 and 5 be the same physical platform, because they are both exit platforms). Entrance platforms I'm more inclined to keep separate, because those will need to be larger.