I'm only answering the questions I have personal experience with; most of the answers to your other questions can be found with a basic Google search (I also suggest looking at discoverhongkong.com).
1. While there are rural areas, Hong Kong is fairly built-up. There is no one "downtown" area, but I suggest anywhere near an MTR stop on the north side of Hong Kong island or between Kowloon and Tsim Sha Tsui would be convenient in terms of what you are looking for (more below).
2. Macau offers casinos, culture, and architechture. I suspect a 2-year old is going to be quite bored.
3. Do you like Chinese food, or Chinese-American food? If your tastes run to egg rolls and sweet-and-sour chicken, you probably want to stick to American and European type restaurants. If you can handle roast goose, fish served with the head on, and tofu as a dessert you're going to have a marvelous time eating in Hong Kong.
4. The MTR ("subway" is more often used in Hong Kong to talk about underground pedestrian crossings) is a very good system that covers just about everywhere a tourist might want to go in Hong Kong except the beaches. In addition there are various ferries that cross the harbor and go to outlying islands, and taxis are relatively cheap in Hong Kong (and very useful when the MTR and ferries shut down for the night). I wouldn't recommend the bus or mini-bus systems to first timers, but the tram across Hong Kong Island is also reliable.
5. MTR stations are accessible, but often there is an elevator at only one entrance and it may be inconvenient to get to from where you are at the moment. If you require elevators, I suggest you go to MTR.com.hk beforehand to map out which entrance is accessible.
6. If you're looking at prices on a Hong Kong website, please be aware that the prices quoted are in the local currency unless otherwise noted. If you're looking at prices on a Macau website, the prices could be in Hong Kong dollars or Macau patacas, but since there's only a 3% difference in them, it's essentially the same.