Jessica:
I think you're making the right decision to pass on the Park Hoppers for your family. I usually recommend that families with small children use that money (that's $54 each plus tax for hoppers....) to splurge on a memory-maker experience they will remember like the
Pirates & Pals cruise, a dinner show like Hoop dee Doo or a Character Meal at Chef Mickey's! Moving from park to park with little ones is tiring, especially with two toddlers and a stroller!
It sounds like you've got 6-Day Magic Your Way Base park tickets, and yes, I would agree that three days at Magic Kingdom may be overkill. Using another day to go to expansive Epcot or Pixar-friendly Disney's Hollywood Studios would definitely be a better use of your time. That way, you can visit two parks at a more leisure pace, possibly even returning to your hotel during those afternoon for nap breaks.
My advice: Visit all four parks and choose which of the three (Epcot, DHS or Animal Kingdom) is worth a second visit and save your last day for your second visit to the Magic Kingdom to end your trip.
If you have any more questions about your visit, feel free to come back and visit me via my bio page! Wishing y'all a magical vacation!
Whitney