I understand your dilemma as we still go through the same dilemma. Our twins are older now (4 yrs old), but we still take our double jogger and it's hard to beat the convenience of the monorail resorts and the Epcot resorts. Either area, you shouldn't need to take your car to parks very often. Enjoy the convenience of rolling your stroller right on the monorail, boats, or else walking to some parks.
Maybe base your decision on which park you think you'll be going to the most? If MK, then choose a monorail resort. If Epcot and Studios, then go with BC. Although you know what? When we stayed at BC and our twins were around the same age as yours will be, we actually did some rides in Epcot and then jumped on the monorail to MK. We rarely had to unload our stroller and fold it up. It was nice because we packed the stroller with all the baby supplies and our kids took cat naps at all different times of the day, so we appreciated the fact that we could just let them remain in the stroller without waking them.
Also don't forget the character meals will be free for your twins, so take advantage of that! We did Chef Mickeys a lot when our kids were that age.
I probably didn't do much to help you with your decision, but rest assured that I don't think there is a wrong decision here. You are deciding between the best of both worlds.