I love Disney Transportation and use it extensively on all of our trips.
Sometimes we drive, sometimes we fly, but when we drive, our car never moves from the parking lot.
We usually stay at All Stars as a family, and I camp at Ft. Wilderness once a year solo. We have eaten at just about every resort, and we DON't spend a lot of time waiting on transportation or transferring to Downtown Disney.
The biggest key is to know the park closing times and use them effectively.
Plan ahead, schedule your meals so that you can have a nice dinner and get back to your resort without a lot of trouble.
For example:
When Studios closes at 7:00 pm - Fantasmic is over at 7:30pm
We make a PS at one of the Epcot resorts Beach Club/Yacht Club, Boardwalk, etc.) at 7:45 pm. Once dinner is over about 9:00 we stroll through Epcot while the masses are watching Illuminations, watch the fountain dance awhile till about 10:00 then onto a waiting bus at the Epcot stop.
When Magic Kingdom closes early, we go to a monorail resort for dinner, then take the Epcot monorail to get to the bus stops.
We also frequently make our mid day break at one of the resorts besides our own. We have lunch, we sit at the pool bar (we don't use the pool) We stroll around the lake, or relax in a garden somewhere.
At park closing, never rush to a bus stop, wait in the park till the masses leave. It is much more pleasant to sit on a bench with a drink and listen to the park music, or watch the Epcot Fountain, watch the castle change colors, watch the lights on the Sorceror Mickey hat (you get my drift) than it is to stand in a line with upset folks in a smelly bus station.
I guess what I am saying is don't try to make Disney transportation work with your schedule, make your schedule around Disney transportation and avoid some of its drawbacks.
The only thing about Disney transport that I have not ever been able to find an easy schedule for is Ft. Wilderness internal transportation. However, I have solved that by taking hubby's
ECV with me when I camp there and use it similar to a golf cart.