Welcome to the DIS boards!!!
Yes, if you make a reservation on Disney's Magical Express (DME) you will go directly from the airport (MCO) to your resort. If you choose to let DME handle your luggage and you put the special yellow luggage tags on your bags before you leave home, your bags will go right from the plane to your resort. Yes, it may take up to several hours for this to happen. So you should pack whatever you may need for the first 5-6 hrs. at WDW in your carryon bag. Or, you can not use the yellow tags and when you get to MCO go to baggage claim and get your bags. Then, you will head to the DME checkin desk, you'll get your vouchers stamped and off to the bus you go. If you have decided to grab your bags, they go with you, underneath the bus. The bus will make up to 3 stops total. The stops are quick, so no need to fear that you will be on the bus for hours on end. In fact, the average time from deplaning to resort checkin is about 70 minutes.
The resort to parks transportation is very good. Buses leave every 15-20 minutes from the resorts. There is a bus that goes to each one of the different parks. It is very easy to figure out where you need to be and on what bus. If you are planning on going from resort to resort for meals or such, it can be a bit more difficult. You have to go to a park, and then transfer to the resort bus that is going to the resort you need. Or you can take a cab...lots of people do that in order to save time.
As far as getting to those off-site attractions...For Universal you can take a shuttle (Mears, about $15 pp, has to be reserved ahead of time), a cab (about $30 each way) or a towncar service ($50+tip, both ways, reserved in advance).
Kennedy Space Center is a different story. It may cost you over $100 to get either a cab or a towncar from WDW. It's an hour away. For this one, I would be tempted to rent a car for the day. You can rent a car at the Dolphin, some of the hotels in DTD, or at the Car Care Center by the entrance to the MK.
Hope this helps and answers some of your questions.
