What seems likely (to me, at least) is a San Antonio-Austin-[somewhere in the middle of the existing route] line. You'd have an expensive junction to accommodate San Antonio-Dallas and San Antonio-Houston trains, but doing so probably saves you something like 50-70 miles of track construction (at a minimum). There's a reasonable chance that adding San Antonio and Austin together (to Houston) at the cost of adding 10-15 minutes to travel time would do better than "just" San Antonio-Houston. Granted, you would ideally find a way to serve Waco, etc. along the I-35 corridor, but I suspect that San Antonio/Austin/College Station would be more than sufficient to support the line in question.