I flew a lot with DD (now 2.5) as a lap baby and a couple of times now as a toddler. Next month we fly with DD and our twin 3-month olds. The babes will be lap-babies and DD will have her own seat.
Definitely bring a carseat for the 3yo. He'll sleep much better, and IME be more comfortable, especially on such a long flight. We have a Cosco Scenera that was cheap ($50) that we use for travel, but DD has nearly outgrown it, so that may not be an option. We use a rolling luggage cart ($20 from Staples) and bungee cord the carseat to the cart. Then DD rides in it like a stroller, or if she walks, our carryon bag rides in it. As far as the potty - it depends on your kid and how well you think he can handle waiting if he has to go during takeoff, landing, turbulence, etc. DD is VERY reliable about the potty, but we're still considering training-pants for the flights.
For the babe, personally, I'd do diapers for the flight. Take her to the potty if she needs to go at a convenient time, change her as often as you can, but I think an airplane is pretty close quarters for peeing in a tupperware. Maybe if you have your own row, but I wouldn't count on that. As far as wearing, keep in mind that most flight attendants will make you take baby off for taxi, takeoff, and landing, and possibly turbulence. They may let you wear her during the regular flight, but they may not. IME it is pretty much luck of the draw.
You can bring the carseat and gate-check it if you don't need it. I'd do that if I needed the carseat at the other end of my flight (rather than checking it all the way through). For our flight, we aren't bringing seats for the boys (we have seats available at our destination). Longer flights seem less likely to have any open seats these days, so we didn't feel it was worth it to bring a seat that we might get to use and that the babe might be willing to sleep in for a few minutes - we'll just wear or hold them for the duration.
Are you traveling alone or do you have a spouse or partner with you? We are opting to not bring a double stroller because there are two of us - toddler will ride in her carseat or the single stroller and each adult will wear a baby and a backpack while pushing a stroller or pulling a carseat on a cart. A double stroller might be more sensible if you are traveling alone, though.