OK, the reality is that you will visit the Alamo no matter what I say so that you can say you've been there, but the missions that are part of the San Antonio Missions NHP are the true gems of the area. You can drive, or if you're over 18 and up for some exercise, rent a bicycle from B Cycle and hit the trail (not yet complete to all the missions - to open summer 2013).
I started out at Mission San Jose, where there is also a visitors' center, and enjoyed a walking tour with a park ranger. He helped put the missions in context in Texas history. As a non-native, that was particularly helpful. Afterwards, I was able to explore on my home and take photos. The grist mill operates some of the time.
From there, I headed on to the Espada Aqueduct, Mission Espada, Mission San Juan before heading back up to Mission Concepcion (closest to San Antonio). Each is a little different from the others in size, style, detail, restoration. San Juan was the quickest visit, least impressive. It takes ~2 hours to drive among them and walk around.
these are functioning churches. The government helps support the general park, but the churches themselves are funded separately through the church.
It's worth a visit! You'll leave thinking, "This is so much better than the Alamo."
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