It sounds like by the nature of your post you are in the same boat as we were, only different.
With 3 adults and 3 kids its going to be a wash which way you go. I might suggest looking at it from another point of view.
How long are you going to be staying there? if it's for just a few days, you might want to do a suite. Kids in one half and adults in the other. Depending on the hotel this should be cheaper than two room's. If your going to be there for a longer period, separate adjoining rooms might provide more sleeping and leisure options, guys & girls, kids or adults or what ever works.
We tried 3 kids and 2 adults in one room for 10 days at the Contempory. We all had a good time but never again in one room. For us a suite will work being all of the same immediate family. We looked into 2 rooms, it was obviously double the price but we could not get a guarantee that the 2 rooms would be adjoining and a suite was not available for or dates requested. So we decided on one room as the Comtempory has the biggest rooms of any Disney hotel. It all boils down to how long you are going to stay and what kind of privacy needs your family requires along with whatever your uncles individual needs might be, compared to what your group can get along with or without for the length of stay.
As with us money is always a issue but we looked at it from the standpoint that we don't get to go but once every 5 years or so and that we would be down to 4 next time. So we decided to spend less for one room, be crampt, and stay for as long as we could.
We loved it, but never again in one room , even with 4.