We just stayed in a Contemporary North Wing garden view room with our two toddlers. It was great being able to walk to MK in 10 minutes! We stayed on the ground level and had the patio. It was also nice not to have to mess with an elevator when you have a stroller. I am considering renting points at BWV (just for a studio though) on our next trip. I would definitely stay at CR again, but I also like the Epcot area resorts. The CR rooms are huge, but a 1 bedroom would be even nicer. I personally don't like to cook on vacation (that's why it's a vacation!), so the kitchen isn't an issue for me. The CR has a nice size fridge in each room (no charge), and we do stock it with breakfast foods, snacks and sandwich stuff. The CR food court and convenience store also have some nice offerings for quick and cheap eats. You might even look into a suite at CR. I'm guessing that the money you save by not booking a 1-bedroom villa, you could easily afford some nice meals or even have groceries delivered to your room.
At age 2.5, your DD won't be demanding to go to MK constantly, like my 4.5 year old, so I'm leaning a little toward BWV. I really don't think you can go wrong with either one.