Now hear me out...
I probably don't have the best ideas but I have been thinking about this. If the LRT gets long enough it may need to be split into two. It's not like there are no long "subway" lines in the world, but Line 5 is uniquely split into a long grade separated section and a long section that is not. The western extension will be grade separated, and the airport leg will (I would only assume) be grade separated. In some future reality the line could even go down the Mississauga Transitway and get a short elevated section to Square One! Meanwhile in the east, any extension will be at-grade. They are even proposing a "Line 7" since apparently connecting directly at Kennedy is too hard.
So why not split the line (eventually) at (hear me out!) Science Centre Station!

All you would need to do is remove ONE at-grade crossing at Sunnybrook Park. It would make Lines 5, 7, and 3 all converge on one station. And it would split the increasingly longer and longer at-grade and grade separated LRT sections.
Or, again, maybe I'm missing something. Like, load balancing or some nerdy thing.
Maybe I'm also just obsessed with having more individual lines with their own numbers. (WOAH, SEVEN!)
Perhaps it's not the best thing in the world to have a linear transfer. But that's what they are proposing at Kennedy anyway + you could probably choose to either through-run or short turn trains at Science Centre ANYWAY despite it being two lines in order to balance service. You would then argue that that means it may as well be one line then, BUT I think:
A) It marks very clearly a split between two lines with different operating modes.
B) If you are short turning trains on a single line, that is awkward for the customer, instead of:
C) If you were traveling east towards Science Centre and wanted to keep going, you already know you have to change trains. An announcement that the train is through-running is a nice announcement, versus the announcement that would be involved in the above example, which would be a negative one informing you that your train, despite traveling on the same line, is not continuing.
That's my two cents anyway.