| I would say the greatest difference between the two universities is Baylor's overtly Christian environment. Baylor offers a high quality education within a Christian environment, which is not for everyone.
As to the quality of education, compare the number of Fullbright Scholars, etc., and Baylor wins. If the student is honors program bound, compare the honors track offerings at the two schools, and Baylor probably wins there, too. Baylor's University Scholars and Business Fellows programs allow the student to create their own course of study with few required courses. Baylor has a larger network for gaining post-college employment and internships, and in many programs, getting into grad school.
Residence halls are probably nicer at Trinity, and San Antonio certainly beats Waco for most people.
Good luck with your choice! | 
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