I was looking into a Disney trip last year to DL for my younger DD's b-day--her fourth. It would have been a mommy and DD trip, only. I talked to the boys, and they were perfectly fine with that. We ended up not going because I just couldn't get a decent flight price. We've taken just the boys, I've taken just DD and we've also just taken the one who had an interest before. As long as everyone gets their shot, their time, I think it's good.
So, I don't think that taking just one or maybe just two, on theory, is wrong. And, I have to add that I think too often these days kids equate the privilege of doing something as their right to do it. Disney would be one of them. I'd have no trouble (well, I'd feel bad, but I'd still do it) leaving a child home IF they were having troubles that I thought were serious enough, AND they were warned. I wouldn't plan it to begin with leaving the child at home. OR, it could be one of those situations where "you can go IF" and then the ones that complete the "IF" get to go.
In the situation you're describing, I would not take two and leave one. I would, perhaps bring one (either the little one--she'll still get the magic and it's even more magical when it's only one OR the oldest one--he has so little time at home left) or make it adult only.
I'd also have no trouble going with just my DH. I'm of a mind that spending time alone as a couple is extremely important in a relationship. We'll go away for a weekend on a yearly or 2x yearly basis. My parents typically take the kids. It's wonderful! We miss the kids, but I would definitely do it. One of my "goals" in the next couple of years is to get my DH down to WDW for the food and wine festival, and frankly, I don't want my kids there! I'd like to walk around WDW holding hands, enjoying wine. Have a meal that didn't include entertaining my kids or kid friendly atmosphere. Sleep until when I wanted to and stay up and watch whatever I wanted to on the tv as late as I wanted to. Wow, I'm already dreaming it! Calgon (or Mickey) take me away!!!
It might be a very nice trip with just you and your sis. Take a long weekend, get some great resies and have a girls' trip! That would be my suggestion!