There are a potentially huge list of factors you could consider to make the "right" choice in this case. Many of them you've listed already, others you haven't. And which ones are most important will vary based on your exact needs. So while I can't offer you a comprehensive analysis I will share a few thoughts:

1. I agree with your general inclination that it's better to arrive in Tokyo at 3:40pm JST instead of 9pm. It'll be easier to transit and easier to adjust to the timezone change.

2. An obvious difference with #1 is that you use up most of your Saturday by departing at 10:30am instead of 6pm. If you've got nothing else important to do on Saturday that's probably fine.

3. I would consider seat availability on both long-haul flights. I.e., is my preferred seat type (aisle or window) available on one but not the other? I'd also note the operating airline and aircraft type identified in each itinerary and reference a service like seatguru.com to learn more about seat configuration.

4. Aside from it being a longer overall trip I see little drawback to taking a connection at YYZ. The airport has an international transit zone so you will not have to pass through immigrations and customs upon arrival like you'd have to if transiting at a US airport.