YES, YES, and YES! That time that the two of you have alone will be the best! AND, it sends the message to your "big guy" that he's still special (in case he's feeling a bit left out with the baby around.)
My suggestions:
1-Stay onsite if at all possible. One, you don't want to suck your limited time up with transportation. You also don't want it to be out of the question going back to the hotel for nap time or down time. If money isn't a big issue, I'd stay at the Contemporary. I remember when I was young and being so excited at going through the contemporary hotel. We stayed once at the Polynesian, and I was so mad that we weren't staying at the cool hotel! The AKL sounds great too, but the Contemporary is just a hop away from MK. I don't imagine the pool will make all that much difference, as you prob. won't have a ton of time to hang out in one. And unless your DS is a good swimmer, won't matter about waterslides and stuff.
2-Make a res. to at least one character meal. For a little guy I'd probably do Donald's Breakfastasaurus or Chef Mickey's in the Contemporary hotel.
3-On the way down, or while you're at the other hotel, sit down with your DS and find out what all of his "must sees" are and see if you can come up with a plan to do those things. What we think the kids' favorite things are isn't necessarily what they are. When I was little one of my very favorite things was going over to Tom Sawyer's and getting a big pickle and PB&J from Aunt Polly's cabin. No one would have guessed that was my favorite, as I was 100% girly girl

! If he doesn't remember enough of the activities, maybe showing/using a WDW map, or prompting him with some of the activities you remember him enjoying.
4-Together come up with "rules" for the trip. I find that ones that they come up with are the best followed. For example, "bobby, what can we do to make sure Daddy doesn't get lost? What should we do if we do get lost?" Set the expectations, go over them again every morning. With only one set of hands, it might be more challenging keeping track of him. It would be very important to me that DS understand that he needs to be able to see me at all times so that I know I can see him, that he holds my hand without argument when I say it's necessary, and that he understands where to go/what to do if he gets separated.
5-When my DS's were little we went to DL and I got the boys and Daddy matching t-shirts. To this day (when it's difficult getting them to even wear the same color!) they love looking at those pictures the best of all our trips. If you're into it at all, your DS would probably walk around like a little peacock that he matched his dad. (Though, for me, it was a safety issue. The shirts I purchased were bright orange--which was great for them and their coloring anyway--and very easy to see in a crowd. Plus, if one of them got separated, I was able to hold the other up and show people exactly what they were wearing. A side benefit, there were a few rides the boys went on without the adults and I found that people automatically grouped them together and if one of them fell behind, other people would say "oh, you'd better catch up with your brother" or "wait for your brother", but only in a nice way.)
6-Make sure you spend time letting your DS look for something special for Mom and baby.
7-And it's totally "out there" but make sure you have the "stuff" needed for a WDW trip. I say that because my DH would just pick up and go and he'd come back with sunburnt kids with headaches and dehydrated and freezing because they didn't have a sweatshirt. When my eldest was 3, he would have NEEDED his lovey for any ride that required him to be brave, too. Things I always have with: A pill case that contains benadryl chewable, children's chewable tylenol or advil, tylenol and/or advil for me and pepto bysmol (I'm sure I spelled that wrong!); change for those various change eating things; sunscreen; rain ponchos; change of socks (boys love those water fountains wet feet lead big time to blisters); sweatshirt/jacket; bubbles for sitting waiting for parades; camera with extra film if it's 35mm, extra memory card if it's digital and an extra set of batteries; and a water bottle to keep them hydrated. I usually have a lot more, but those are the essentials to me.
Enjoy!!! I'm jealous!
