Here's a few suggestions that might help. My Gf also has a 12 YO son, we have been to WDW once and DL many times with our AP's. There is no younger child but he still doesnt want to do some things, and he can be quite difficult about it if he wants. WDW we took grandma and she hadnt been in years so she was like the 4 YO on that trip, so give this a try.
If hes like all the other 12 YO's he wants to be considered a "big kid" and not a little kid. Take him aside and have a mom and man to man talk with him about your trip. Tell him how mature he is and that he isnt a little kid not like the little sisters are. Tell him you expect him to live up to that while on vacation. Explain to him that this is a family vacation and it is for everyone, not just him and that you and dad want to spend as much time together as a family because he is growing up so fast. (stroke his ego a bit) Explain to him that he is going to be asked to do some things at WDW that are not his favorite, some things that his younger sis's will probably enjoy more and you are really going to appreciate his cooperation. Make sure also he knows your also going to do the things he will find fun, he just needs to understand that he might have to show how mature he is by waiting and not doing those things right then and there and he might need to do a character dining or ride a couple of kiddie rides in between riding the big rides. I have found that while he wont admit it my Gf's son will ride and enjoy alot of different things. There are only a couple of things he will really refuse to do and we will often ask him what he wants to do, once he answers we will tell him "do this with us then we will go do that with you" a trade off sort of thing. Another option we have used is to find him a bench to sit on and tell him to stay there while we ride, dont move and we will come back for him after the ride. Often the thought of sitting there alone for half an hour or more is a motivator to get him to ride. If he gives you a hard time tell him he can stay in the room alone while all of you go enjoy the parks, no TV, no video games, just sit there, this can also be a motivator. Spanking can work also, and some kids do need it, but I have found a good talk works best. But get him ready for the trip by talking to him in advance, agreeing to cooperate then remind him when you arrive again how he is no longer a "little kid".
make sure also to praise him for how grown up he is acting, you might even suprise him with something he wants or wants to do for being cooperative.
You will need to split up and I really reccomend it anyway. Each of you take some time with each kid for some one on one time, especially the 12YO, take him to do some of the big rides, just dad and son and mom and son, let him choose what rides and maybe a fun snack. Your youngest may not remember but your 4 YO will so its important to have some one on one time with her also, let her pick what to do also. The afternoon naps are a great time for this, one of you can take the little one/ones to the room for a nap while the other spends a few hours with the older one then switch off. Let him know ahead of time your going to do this so when your all at the parks early he knows there will be "his time" later in the day. You really might be amazed by him when its just the two of you hittin the parks together. Also, while you may be planning things out like what parks to do on what day and where to eat, let him choose a place to eat for at least one meal. You might be suprised, my GF's son will always choose Goofy's kitchen which is a character dining. Make sure you explain to him that character dining is for everyone, not just little kids, he doesnt have to get his picture taken if he doesnt want to but you and dad will really appreciate it since he is so grown up now. And ask him who his favorite character is and tell him you really want him to meet the character and get a pic of him with them. Hes old enough to get more involved in the planning so do it.
Most of all, take your time and have fun. Dont give anyone the power to ruin your day or your trip, thats way to much power to give to anyone.
Steve