"did you do the Bruce Peninsula Trail"
I haven't done much of it...just a few small sections at the north end in Bruce Pennisula National Park.
I really don't know enough about this trail to pass judgement on it, but I will say that my uninformed impression is that it goes through an awful lot of developed areas. It certainly links together some nice spots, but it doesn't seem like you'd get much wilderness on this trail. Southern Ontario is all farmers fields, roads and urban sprawl, so hiking through that via a narrow strip of forest never made it to the top of my to-do list. I'm sure the Northern half has some really great areas though, once you get away from Hamilton and the GTA (greater toronto area).
I personally would look at Killarney and Algonquin first. Algonquin gets busy, but it's got a LOT of nice backpacking trails that take you by some awesome lakes with great fishing. I suggest the Western Uplands area of Algonquin, which has options ranging from about 30km to 88km. Start at highway 60: