The only thing about a car is that you most likely would have to end up paying for parking at the hotel, which can be very pricey.
Advantages of DLE: It's the most comfortable. The seats are big and roomy. They show Disney movies on the bus. It's the most "Disney." It can also be the cheapest if you have kids -- they don't charge for under a certain age (maybe 13 or so, I don't remember for sure). Car seats are not required.
Advantages of Lyft/Uber/limo -- quickest. No waiting for the bus (as you said, it could be up to an hour) and it goes directly to your hotel. If you take the DLE, you only go directly to your hotel if you are staying at the DLH. Otherwise, you go to all 3 Disney properties first, then to other hotels. Same is true on the return trip -- unless you are staying at the DLH you will have stops on your way back to the airport if you take the DLE. Lyft/Uber may be cheaper than the DLE if you have more than 2 adults. Limo will be more. Also using any of these services you could stop somewhere else (like a grocery store) on the way if you wanted.
You can also take a shared shuttle, which would be somewhere in between. Less comfortable than the DLE but may be cheaper. I'm not sure how often they run but it has to be more often than the DLE. No stopping for groceries.
Of course the limo would be the most expensive but probably the most comfortable and quickest. But no movies or theming.
We tend to take the DLE on our way to the hotel because we like getting a "head start" on all things Disney and we usually stay at the DLH. We sometimes use another way to get back.
I do have to mention that our last DLE trip was less than stellar, however, as the A/C on the bus was out and it was August. I think I read someone else say the same thing recently.
At that time of night I have no desire to wait for a shuttle. 
