You cannot go wrong with either, both very interesting places to visit and UNESCO world heritage sites. If you can only visit one place, my advice is to look at images and You Tube clips and select the one which draws you in most.
Visit the roman museum in merida.
I love to see the Roman Museum in Merida. This is an astounding museum that should be seen.
In Merida you can buy chocolate covered figs that are called "higos".