Hi there! I would choose either CR or AoA. Here's why:
1. CR is fabulous. It has the monorail going right through the lobby (which is fun to just sit and watch!), and both the TS and QS options are awesome. We have stayed in a Garden Wing room, and we had a first floor room with a patio and view to the water pageant each night. The room was spacious with three sleep surfaces (two queen beds and a roomy daybed pullout) with plenty of room for a pack n play too. The bathroom is laid out well; we were able to have someone showering, someone brushing teeth and someone using the separate potty area all at once. The Garden Wing is quiet, yet a quick two minute walk from the hustle and bustle of the main tower. You can either take a fun monorail ride to either MK or EP, and you can walk to MK easy peasy. This would be an ideal resort to take a little one back for a midday nap, or bring the whole family back for a rest time/break midday. The busses to HS and AK are absolutely fine...for my kids when they were young, the bus ride was half the fun of a WDW vacation.
2. An AoA family suite is fabulous. There are three sleep surfaces, plus plenty of space for a pack n play. Bonus points for two FULL bathrooms, a kitchenette, and a master bedroom where a little one can nap/sleep while the rest of the family hangs out in the family room/kitchen area. The theming is awesome if you have Cars lovers...we stayed in a Cars suite, and the whole area makes you feel like you've walked into the Cars movie. We spent most of our time in the Cars pool area as it was quieter and we could have a Cozy Cone cabana all to ourselves. While there are no TS options, there is a food court, and the food court is great, and you can walk over the bridge to visit Pop Century and their food court (which is nice too). You would have the gondolas to get to HS or EP, plus dedicated busses elsewhere.
I would NOT recommend a split stay with your three kiddos. Way too stressful, and not worth the unpacking/repacking. Seriously, the transportation (bus and monorail) was half the fun with our young kiddos.
My final recommendation: you will have a WONDERFUL trip wherever you stay. However, I would recommend an AoA suite for your first experience. You will definitely want to come back for future trips, and staying in a deluxe the first time might ruin you!

Maybe try AoA, and try a deluxe (CR is one of my FAVS!) for next time?
I know you will have a magical trip!!
