Thats one of the most asked questions I have ever heard, and I always reply with the same answer, it depends :)
Neither city is just better than the other one, they both offer different things for its residents and it depends on what you are looking for to decide which city to choose (including any other cities you want to include).
I first lived for 1 year in Toronto, now spent 2 years and a half in Mississauga and going back to live to Toronto. The reason? What I'm looking for has changed.
Toronto is specially good for single people and couples with no children, Mississauga on the other hand is great for families with children. I have loved my time in Mississauga, really peaceful and everything you need, but it can become a little boring when you just want to go out really quick to have fun, or want to go to the gym without having to use the car, or want to spend the night out in a club.
So again, it completely depends on what you are looking for ;)