I'd like to change my vote depending on the answer to a question. All of my experience in camping stems from canoe trips. I have no background to rely on in terms of a hiking scenario. Most of my trips surround the North Tea/Biggar/Manitou lakes in Algonquin. All very large lakes in comparison to the trip we are talking about here. But the portages are relatively short and well travelled. My trepidation on the other routes stems primarily from the difficulty these portages represent or more to the point may represent.
What are the portages like on the routes that have more/longer ones?
If they are similar to those found in the Northern ares of Algonquin then I would say I really have no preference in the route taken. Other then to say that larger lakes will invite more wind and potentially less bugs. Trips on smaller lakes though safer in a storm tend to be more buggy and muggy in warm weather.