Hi Danielle,
Disney in the fall will be cool. The humidity will be gone and you can experience temperatures in the low 80's as a high. All of Disney's pools including the water parks are heated to 82 degrees so it really is up to you if you want to hit a water park. Personally, I think it is too cold to even swim this time of the year.
Look at the cost of adding the Water Parks Fun & More option to your ticket. If you are going to go at least two times to the water parks, it might be worth it to you. Plus you would also get DisneyQuest and golfing as options as well. Your children are little and that is a lot of activity to plan for a vacation. I know my children did not like going from 7:00 am to 11:00 pm daily. If your can not do those long days, than skip the extra ticket price and pay for the water park separately if it gets hot. Also, the Disney pools are really cool and fun and most kids are happy at their resorts pool.
If you did plan on going to a water park,
Blizzard Beach is the one to pick for this age group. There are lots of family rides and Ski Patrol Training Camp is perfect for them.
Wishing you a magical vacation!
Beth