Hi and welcome to disABILTIES.
There are many rides where she can stay right in the wheelchair for the attraction and I would highly recommend that. I can't psot a link from the computer I'm working on right now, but if you go to
www.wdwinfo.com and look under the Theme Parks area on the left side of the screen, you will see alink for "Disability Information". The page that link leads to has a list of rides where a transfer is not necessary to experience the ride/attraction.
She may transfer by herself, but she probably doesn't transfer anywhere near the number of times that she will at WDW. Another thing to think about is how long the ride is. Some of the MK rides are only 2 minutes long - much harder to transfer back out again than a ride that is longer. You can get ride length information from the GUIDEBOOK FOR GUESTS WITH DISABILITIES, available at Guest Services at any of the parks or on-line at the official Disney site (I will post a link after I get home if no one else has done it).
You are right that how hard it is to transfer depends on the ride. For example, the Pirates of the Caribbean, Splash Mountain, The Maelstrom in Norway, the ride in Mexico and Small World are all boat rides. Small World and Mexico have a wheelchair boat that a wheelchair can roll right on to. The others all have boats where you have to step over and then step down onto the seat of the ride and then step down again to sit on the seat. Splash Mountain has a pretty tight car to get in and out, so even though the rides are all boats, they are not all the same.
Many rides have moving walkways for gettting on and off, but CMs can slow them way down or stop them for baording if necessary (the exception is Peter Pan - that ride can't be stopped for boarding).
I do have one resource (an out of print disability book) that has more specific info about sizes or car doors, etc. Between that, info I have from lifting DD onto rides and experiences that people will share on the board, you should get some good info for planning.
Are there any particular rides that she wants to go on? Also, can she walk a few steps or does she do a sliding transfer? Are her arms affected or mostly her legs?
Thanks for further info. THat should help you get the best answers to your questions.