My wife and I have been to Disney World twice, the first time with our two boys and the second with the boys and both our moms, so on par with your 4 adults and 2 kids.
For both trips, we booked everything through Disney - the flights, the rooms, the bus from the airport to the resort, everything. Mostly because it's the easiest way as there's only one check to cut and everything just works. Disney really does have everything down to a science.
As for the "extras" like Park Hopping and dining plans, obviously it's your call but here's my take on it.
Park Hopper - The transfer from one park to another (I believe MK or Epcot to Animal Kingdom) was a huge pain in the ass. Unless we did something colossally wrong, there was no bus that would take you straight from one to the other. You had to be taken to a central terminal and wait for the bus you needed to show up, which for us was
at least 30 minutes, plus travel time to and from the terminal. That killed no less than one hour of prime ride time with a 5 and 7 year old. The second time we went, we skipped the Park Hopper and just spent one day at each park. It was SO much better that way.
Dining Plans - Both times we've gone we've done the dining plan, again because it's easy. You cut one check up front and you know that your meals and snacks are covered instead of paying another $20 for a few snacks and $50+ for lunch.
Bring water bottles and if you're not a fan of water, bring something like MiO to flavor it. That $4 bottle of flavoring will last the week and save you tons not buying drinks. We've done that on our last few trips, including the last one to Maui and it's worked beautifully.
I'll second bringing ponchos. If/when it starts raining, they'll be sold out in minutes. Or you'll only get 3 when there's 4 of you and your wife will have to take your camera backpack and you'll be soaking wet by the time you're at the car/bus/vehicle.
I will also second Universal Studios. For me and my boys, it was WAY better than Disney World. The rides were right up our alley. The only downside was my wife got food poisioning when we ate at Krusty Burger, but that's because she had a salad.
One does not make friends with salad.