We stayed at WL in 2001 with DS10 and DS7 and they loved it. We then were at AKL in 2004, and my kids were now DS13 and DS10, and they loved it there, too. They're very similar in the level of resort they are, but there are a lot of differences, and it'll just depend on your own kids and what they're like.
WL has the awesome Whispering Canyon Cafe restaurant -- lots of fun, and we all enjoyed it. Big portions, lots of hearty food. We went to Artist's Pointe for a character meal, and it was good, but other than the character meal it was probably too fancy for me and my laid-back kids. Roaring Forks was great, we went down there a lot -- it's more our speed, believe it or not. And quick -- that mattered to us. The WL pool was fun, we enjoyed the slide, the hot tubs, the beach, the boat rentals, the geyser, and the boat ride to MK. I don't recall having any problems with the SL bus transportation to the parks, though I see posts about that from time to time. The resort is beautiful, and the lobby is breathtaking.
AKL also has a beautiful lobby. My kids got me across the bridge suspended (I think) from the 4th floor -- I'm afraid of heights, they're not -- but it's just as awesome as the WL lobby. The pool is probably bigger, but for some reason didn't wow us as much. The slide did nothing for us. Restaurants are really good, but my DS10 didn't like the food much (got sick once, too, near the end of our vacation) -- too different from his American food Dad makes at home! My DS13 loved the buffet at Boma, and the Mara was fine for all of us, but the issues my DS10 had with the Boma food being different made life interesting. It's really good food, and there is some American food on the buffet, just not a lot. We all enjoyed the great fruit smoothies at Boma. AKL has the savannah, though, and if you go to AKL you MUST have a savannah-view room. There is nothing like going out on your balcony and saying good morning to a giraffe, zebra, and I can't remember what else -- lots and lots of animals though! We really really liked that, especially my kids.
Bus service from AKL was good - no problems. It was a looooooong walk to our room, but given the view of the animals we had, well worth it and we didn't mind.
Regardless of which you choose, you will be very happy with your choice -- don't worry about it. If it's not a surprise, just ask the kids and go where they want -- you'll have a great time wherever. If I were to choose right now between the two, I personally would return to WL first.
This year, we went to CBR -- different for us, our first moderate -- and my kids insist that we have to go back to CBR, they enjoyed it so much. They loved the beaches, the boat rentals, the walks around the resort, the food court, all the pools.... so I guess you never know!!
Have a great trip!
You will love either one I'm sure. 
