We have done October and December. We were there in October '09 when it was unseasonably hot and December '10 when we had to wear hats, gloves and winter coats. We have a 4 year old and given either option, I would choose unseasonably hot in October! With that said, there is nothing quite as magical as Disney at Christmas, but you have time and can wait until they are older and more tolerant of the possible cold weather. I would suggest late October -- less busy and a little cooler (80's).
MNSSHP is fun. Our son has gone at 2, 3 and he will go this fall at 5. So far, most of the fun has been getting pics with the characters in their halloween attire. My son finds the parade to be a little scary. It is also a late event, and for the money, I am not sure it would be worth taking 3 under four.
F&W is great! We always have liked Epcot with our toddler, because we can usually get him to nap mid-day in his stroller. The Disney rental strollers are not comfortable at all, so I would advise taking your own or renting a better, more comfortable stroller from a local rental company. When it's hot, toddlers enjoy playing in the water area on the concourse to the World Showcase. My son also can spend hours watching the trains in Germany as well as watching the monorails come by.
You are already past the 11 month window for your home resort and are already within the 7 month booking window for parts of October. The Epcot area resorts are tough to get into for October (I know. . . we are wait-listed currently!). If you go in Oct, you will want a resort with a good pool for toddlers. We have only stayed at Kidani and SSR, so I can't make specific recommendations, although the pool at Kidani is nice. It has a zero entry, which is great with little ones.
Must-do's: Nemo the Musical, Festival of the Lion King, Honey I Shrunk the Kids playground, Boneyard at AK, Fantasyland (of course). Unfortunately, Toontown is closed currently.
Also, if you want to do character meals, you should figure out which ones and call at the 180 day ADR window. These can go quickly! We enjoy The Crystal Palace, Tusker House, and Chef Mickey.
Have fun planning!