With my household of teen/tween boys, I know from experience that having more than one bathroom is a priceless gift. The extra space is also very nice since my sons tend to get on each others' nerves more easily now.
However, when I asked them what they would prefer, they all said Wilderness Lodge. When I asked them why, they said with bunk beds they would each still have their own beds so it would work out okay. They also agreed that the Wilderness Lodge is just "awesome" and worth staying it.
Over the last year we have had two trips to WDW. One was at a two-bedroom villa at the Animal Kingdom, and the other was a guest room at the Grand Floridian. While I love the extra space of the villas, I did miss that our family spread out and didn't really interact much when we were at the resort. When we were in a regular guest room, we were all together talking and enjoying (well, most of the time) each other's company.
Another thing to keep in mind is the general layout of the resorts. The Wilderness Lodge is housed within one building with one bus stop. The Caribbean Beach Resort is made up of 33 buildings with, I believe, 8 bus stops. There are smaller moderate resorts, however, if you'd like some other options.
By the way, have you looked at the
Cabins at Fort Wilderness? This moderate resort combines the space of having two rooms at a moderate resort with similar theming of the Wilderness Lodge.
Just an fyi, your question was cut short; please let us know if we can help further.