If you get all the way to Alberta then you should at least go to Banff, Lake Louise, and then head south into Montana and then east. Getting all the way to Alberta and not taking that route would a big mistake. If anything whip through Saskatchewan (you won't miss much) and spend more time in Alberta.
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Having just visited Banff, Jasper, Yoho, and Kootenay, (and Glacier (Canada), Glacier (US), Mt. Revelstoke, Elk Island, Prince Albert, Riding Mountain, etc., etc.) I would give a complete pass to Banff and Lake Louise, go up the Icefields Parkway, and see Jasper. I thought it was much nicer, and not nearly as developed as Banff. A lot of the grain on my drive back looked to be bear peak already, and the alfalfa and hay was in he process of being mown and baled, if those shots appeal. Riding Mountain and the Upper Peninsula of Michigan were starting to show color in the Aspens, and I suspect will start to turn in earnest this year sooner rather than later.
My Nova Scotian friend says that peak colors in the Maritimes are usually around Canadian Thanksgiving, in October, though I could not say myself (colors in Toronto have not been good since I mived here).
If you want specifically to do the Trans-Canada, fine, but I thin a more northerly route would be nicer for Canadian scenery, or a more southerly route for better chances for color. I very much enjoyed taking a Northerly route through Alberta and Saskatchewan, but the endd of October seems a bit late for those areas. If you are going to be near Sudbury, check out Killarney Provincial Park--nicer than most of Canada's National Parks, imo. Further along, Pukaskwa NP has a beautiful shoreline, though limited access without a boat.
