No by 2000 Eatons was long gone too. Eatons opened as Horizons (their discount value chain) when the centre opened. It opened on the second (third floor) where Toys R Us and Goodlife and the Pickle Barrel currently are. It had that entire floor. This is why there is that lone escalator near the Metro that goes only one way (up). This was the entrance to Eatons. The eastern half of that floor (where the steps to Indigo are and the movie theatre ticking concession) didn't exist.
Indigo was purpose built along with the movie theatre in... 1998/1999 (approx), creating a new mall corridor running N/S from Rexall to Urban Outfitters (at the time HMV). I think the Eatons was one of the original reasons the mall's layout has never really quite worked.
This is why I call the place the Frankenstein Mall. You have the 1970's brutalism, with the late 90's PoMo futurism, coupled with the 2015 green glass box.
As for the square - I personally think it was irredeemable (mostly due to weather and wind - it was probably the windiest place in the city).