Consider one of the Hyatt Resorts in central Texas. Both the San Antonio (Hill Country) and Lost Pines (outside of Austin) properties have wonderful lazy rivers that can entertain a 3.5 year old all day, great golf courses and nice spas for Mom and Dad to enjoy (and Camp Hyatt as well.) They also have lots of kid-friendly activities and kids' movies on the big screen at night. The San Antonio resort is just across the road from Sea World (which is quite different from the one in Orlando) and you can also visit the Riverwalk (as another poster suggested) about 20 minutes away. Six Flags Fiesta Texas is another area option, but a child that young cannot fully enjoy the rides there. Both Six Flags and Sea World have nice water parks to help beat the Texas heat.
Lost Pines is somewhat remote (between the Austin airport and Bastrop), but they have a similar lazy river pool with an artificial beach area, pony rides and it is adjacent to McKinney Roughs nature preserve. They have some interesting programs (free) on Texas wildlife, native Americans, stargazing and trips on the adjacent Colorado River (not free). It's also less than 30 minutes from Austin where you can find some good food and museums, including a nice Children's museum. In summer time, don't miss the nightly bat flight of the world's largest urban bat population from the Congress Avenue bridge. Check out the activity schedule online or call the Concierge for current activities before setting your dates.
With 5 nights, you could consider splitting your stay between the 2 properties, flying into one city and out of the other. Check out the activity schedules online or call the Concierge for current activities before setting your dates.