I'd echo this recommendation. Generally there's no additional fee to rent at MCO and return at the Car Care Center. We've done that many times. You'd save a couple of hours at least on the pick up side of things (skipping Magical Express, driving straight to your resort or even straight to a theme park, no need to deal with shuttle to Car Care Center, etc.).Is there a reason you are picking your car up at the car center instead of the airport. Usually the airport would be faster pick up time, no shuttles, no DME, etc. You could go straight to MK if you needed to. If your worried about time it might be something to consider.
We've only rented a car from the car care center once, years ago. We had no problem with pick up, went smooth, but drop off was a different matter, we waited forever at the counter.