First of all, we stayed at the Wyndham Palms on our most recent trip in early April. If the house you get is anything like the 6 bedroom place we got for our party of 10, you'll love it. You're really close to Disney MGM. Epcot and AK aren't much farther away. Only MK takes a bit of time to get to. And we found it nice to just totally be away from the parks and removed from the Disney stimulation whenever we headed back home. All the houses on site seemed to be very roomy and beautiful, although I was only able to go inside ours. But I'm sure you'll really love it.
Regarding how to make an itenerary--we went with four kids two of whom were small (3 1/2 and just barely 2 years old.) Breaking up touring days with some off time was helpful. We did three days where we incorporated "nap times" back at the house into our plans, two days where we went all day gonzo at the parks (the kids surprisingly stayed awake) and were usually done by 8:00pm. And we took an entire day off right in the middle to do nothing.
I like SeaWorld and if you've never been, it presents a nice alternative to Disney. It's slower paced, more hands on (if you like that sort of thing) and is mostly show oriented.
But if given the choice of a Disney park over Sea World, all four kids in my party would unquestionably choose Disney.
We did AK and the kids had a blast. They have some good shows, great animal trails, the Safari ride is cool, and there are CM/animal experts everywhere--some even have animals to pet, touch or get a good close up look at. My family went in with a bit of hesitance, not quite sure what we were in for, and came out loving the place. Definately see the parade--it's one of WDW's best ones--and take your kid into the Boneyard play area (just make sure to go over all bridges so you can find the giant sandpit/excavation area). Also we saw more costumed characters out in the open at this park than at any of the other four. So if you think your little one will be into seeing "guys," this is the place to do it at.
We also had great success at Epcot. Most of the attractions are pretty mellow. A lot of the park is about stopping and looking around, taking in the surroundings, finding an obscure show or info booth. Spaceship Earth is one of the few rides we did twice at WDW. Our family also really liked shows like Cranium Command and Food Rocks--perfect for smaller ones.
Disney/MGM really only merits a half day for little ones--the Playhouse Disney Show, Mermaid Show, Beauty and The Beast Show, Muppets 3-D, and Honey I Shrunk the Kids Playground are really the only age appropriate things. Most of the rides will be too scary or intense--although the grown ups will think that Tower of Terror and Rock 'n' Roller Coaster are great.
You'll at least need a day and a half at MK--that's what we needed. And it's funny, with our party, no one really got obsessed with needing to do a ride for a second time just after riding. We found that having something else spinning, whirring or whizzing by within eyesight always inspired a "let's try that one" response. I guess it depends on the kid. Ours were really into a "what's next?" mode.
Good luck and Have fun!