Portaging is my favourite thing to do with a canoe. Not so much because I love to carry a canoe (but I think I do), but more so because of where it takes me! I can get deep in the wilderness without the sound of motor boats around to disturb the peace. I also just love the feeling of independence I get after moving myself and a bunch of stuff deep into the bush and back out again!
You'll want to plan your trip, though. You should have a decent idea of how fast you'll be canoeing, and a little wind or going against the current shouldn't throw off your estimate too much! Few things are worse than being in the middle of a lake with the sun setting with no campsite in sight.
You can use topographical maps to get an idea of which direction the current flows on the rivers you'll be paddling (water flows downhill, of course!) but the current shouldn't affect you as much as the wind. Big lakes have nothing to shield you from the wind, so you'll get blown around hard. Paddling against heavy winds is difficult and can be very frustrating.