US 50 has far more traffic. And the towns along the TransAm are used to cyclists and very welcoming.
KS 96 has, on average, about 1000 vehicles per day across western Kansas.
US 50 has at least 2000 in most places and more than 4000 near the larger communities.
Personally, I prefer Nebraska - but if you are riding across Kansas, the TransAm is best.