Its been discussed in detail here but the cliff notes:
1. In the original design they simply didnt think about it, Transit City was "median city", running the trains down the median of the street, always. (we can debate why that is but I have my own opinions on it ill leave out for now)
2. As projects progress they go through many revisions. In revisions and a more detailed EA to Crosstown, several alternatives were floated, including putting the stop and tracks on the south side of Eglinton.
3. Rob Ford attempts to bury all of the Crosstown underground.
4. In order to stop this, council votes to go back to the original designed plan of the Crosstown. It passes.
5. Because of this, any modifications to the original design of the Crosstown would allow Rob Ford to reopen the debate and attempt to get the line buried again.
6. In the best interest of moving the project forward and stopping any more political interference, its decided to do the plan as-is, flaws and all.