My thoughts as someone who has been several times with small children...
Since you are staying at a Disney Resort, remember that you are a guest of Disney and entitled to all the benefits of any guest regardless of the quality of the room. One of my favorite tricks is to drive up to the Boardwalk 5 star hotel, let the valet park my car for free after I pull the strollers, etc out, walk through the hotel lobby to the man-made lake, stroll along the tree covered paths and enter Epcot via the secret side entrance. No hassles, no monster parking lot, no fussing children when the park closes if you stay that late.
One note for your daughter: If she buys a season pass for a few hundred dollars, Disney will knock around 50% off the room rate. That trick has saved me hundreds of dollars and a recent co-worker used it to save over $1000 at a premium resort. Plus a standard ticket will run you serious money so it's not that much more. Only the person making the reservation needs the pass.
If you only have two days in Orlando and you are paying the premium to stay at Disney, you should spend them both at Disney World instead of branching out. Disney just has an insane amount of stuff to do and as a guest of Disney, you get into selected parks early each day. If your ticket allows re-entry, consider going first thing in the morning, leaving at lunch for a nap and pool time and then going back in mid-afternoon. The parks are usually packed around lunch time and you can save some money eating outside the park. If your ticket allows park hopping, consider eating dinner at Epcot where the restaurants are excellent (if pricey). Make dinner reservations in advance.
If you still want to branch out, Sea World is the top pick. Universal Studios is great as well, but not so much for a four year old. For the same reason, skip MGM at Disney. The Disney area has waterparks you can pay for and some of the resorts there have excellent pools that you can use for free (see "guest of Disney").