Since you asked...
My opinion is that you need to sit down and run through what you anticipate an operating session would be like for each of the three layout. You need to do some thinking about what kind of scenery you anticipate having, including if applicable industries that would be served by your trains. You need to think about how you are going to access each point of each of the layouts. I know you say you like running more than yard work and switching. That is how you feel now. It may not be how you feel three years from now. So you also should be thinking for each layout how difficult would it be in the future to add passing sidings, industrial spurs etc. My final thought is that you say you will be running traditional sized locos and cars and don't need to accommodate scale sized locos and cars. That being the case is O-48 necessary? What options would be available if you decided to go with tighter minimum diameters?
For pure running I think option #2 is the best. Option #3 OTOH gives you the option of parking a train or string of cars without losing operating potential. That's just my view though.
