We are staying in The Wilderness Lodge Resort...mainly because growing up when we went on our family vacations to WDW we stayed in an RV at Fort Wilderness...so it's really a sentimental thing and it's like 'home'.
We plan to just have the limo take us over for the ceremony and then just use our chartered transportation for the wedding to get us to all the wedding day events and back to our hotel. We love any of the resorts that are on Bay Lake as it just makes getting to Magic Kingdom really easy and enjoyable! But, that's just how 'we' like it

You have to do whatever makes you comfortable that you know you would have transportation to and from without too much hassle.
We chose for our guests the Wilderness Lodge, Fort Wilderness Cabins and POR - we thought the idea of having their resort options 'close' to each other would help if anyone wanted to meet up! (some of our guests are taking their cars to WDW)