I've done Saratoga with my kids when they were around 3 and 1. That bus ride back can be pretty rough with two beat little ones—so much so that they're now 3 and 5, and we try to stay on the monorail for the most part. We bought at GF and are having a real love affair with the Poly lately. Of course, as I write this, we have an upcoming trip in November with some friends and are staying at Saratoga because we need a 2BR, though we are still wait-listed at WL.
Saratoga is pretty spread out, whereas if you are at WL, you stay in a much more traditional hotel. The trade-off is that you get a bit more space and quiet at Saratoga. But if it is a rainy morning and you need to get a coffee from QS you'll be outside when you leave your door at Saratoga.
If your family is pretty get up and go, and you plan to go to MK on those couple of days, then I think the boat ride and shorter bus ride to WL are certainly worth it. Not to mention, WL in the fall and winter is pretty magical, with the big fireplace and the tree, on top of being a truly great resort. The theming and vibe are top five on property. I will be ecstatic if our waitlist comes through for November.
$700 is quite a bit of money, though, I must say.