Hello, Kristin!
You will be in for such a fantastic treat if you book a trip to Walt Disney World during Epcot's International Food and Wine Festival as well as Magic Kingdom Park's Mickey's Not-So-Scary Halloween Party! What a great combination of events!
Now, regarding your accommodations, if you are comparing Value Resorts to Moderate Resorts, consider your needs. If a slide at the resort pool is not yet a "must"; then you don't need to look at Moderate Resorts, which have pool slides (the Value Resorts do not.) Next, what is your 3-year old interested in? The new
Art of Animation Resort has some fantastic options such as Finding Nemo, Cars, The Lion King and The Little Mermaid sections, all of which will be open as of mid-September, 2012. On the other hand,
Disney Story Rooms, available as Pirate Rooms at Disney's Caribbean Beach Resort or Royal Guest Rooms at Disney's Port Orleans Resort-Riverside may have that extra magic you are looking for in your upcoming stay.
Now, regarding the lightest crowd levels, I took a look at touringplans.com, an unofficial site which specializes in predicting crowd levels at WDW, to see where the two events you've mentioned are both available, and the crowd level seems lightest. Essentially, you have from 9/28 until 11/2 to be able to sneak in both events. I'd suggest Monday, 10/14/12 through Friday, 11/2/12 as the time to take your trip because the crowd levels seem lighter on more days during these dates than earlier weeks. Of course, weekend days are often a bit more crowded in WDW, especially Magic Kingdom Park, so if you are planning on spending a day to relax at your resort, pick a weekend day to do so.
Please send more questions as you continue to research your options for booking a fantastic fall trip to WDW! I'd love to help!