Another vote for drop the pool day and add EPCOT. My DD loved EPCOT at that age, Nemo ride, Figment Ride, Living with the Land, Boat ride in Mexico, characters. You never know with pre-schoolers until you get there how they are going to react at WDW. Mine was high energy and loved the parks-- she would not have stood for a pool day knowing the parks were there. She had no interest in the pool at the resort when she could swim in our neighborhood pool at home. She was a bear to wake up in the mornings (same at home and same now years later), but once she was fully awake- she was standing at the room door with her stroller telling us to hurry up so she could get to a park. She also hated AK and was begging to go back to MK or EPCOT after an hour or two, which surprised me because she loved the zoo at home- Basically her thoughts were-- I can go to the zoo and see animals at home-- where are the rides and princesses? Some kids love AK- she was not one of them.
You never know what they are going to like until they are there. Mine loved character meet and greets way more than rides- although she did like the rides. She loved the shows. You can always go back to the resort and have some pool time if you want, but that might depend on your kid's likes and attitude. I only recall mine throwing a couple of full fledged fits at WDW. One was our first day when she was 2 when we made her leave the park mid-day to go back to the resort to nap-- we quickly learned that stroller naps and open to close park days were her thing. She had zero interest in going back to the room to nap (stood behind the curtain and wouldn't even look at us for 2 hours she was so mad- no way she was going to nap). Those mid-day breaks that others swear by here, were not for her. The other was when she realized we were getting on the boat from MK to go back to WL to catch Magical Express and go to the airport to go home-- she did not want to leave. (There was a 3rd that involved Barnstormer and her not wanting to get off after riding it 14 times in a row). Mine was typically better behaved at WDW than at home.
I would plan for all 4 parks with the 2 days at MK, and then just plan on being flexible. If he really takes to the parks, you might just stay there all day. If he seems overwhelmed, you might want to go back to the resort and go to the pool. With a toddler, you just kind of have to be flexible and let them take time to smell the roses. It is interesting to see what draws their attention.
DD is 16 now, and she actually still remembers quite a bit from her 3 year old trips and even her 2 year old trip. It really doesn't matter what he remembers though because YOU will remember-- we had a lot of moments from those ages that I will never forget. They are my favorite trips. Plus, they are having an incredible time in the moment, and you will have pictures he can look at later if he doesn't remember.