General Tips:

You CAN have plots in a natural looking down. Just make sure its not a grid. Find areas that are already a little flat and make the plots scattered randomly throughout the land. Make sure you have strict building rules so nobody builds an ugly cobblestone box.

Alternatively, you can build houses yourself and in a way that allows buildings to be integrated smoothly into the landscape, and sell those. Due to the nature of the mesa biome, I'd suggest cottage-like homes, or hobbit-holes.

Of course, if you want to leave it mostly untouched (what I would personally want), you could simply put a little town hall or town square in the middle, make a giant spiral staircase in it, and put your entire town underground. You may need to hire someone with an eff7 pick or get one yourself if you don't want to spend months on it. Think of a large cave with a city in it. Not a series of tunnels.

You'd have a double tourist attraction too. Awesome underground city + Untouched mesa wilderness.

 

As I am building a medieval town, I'm in the same boat as you. Do what I did. Don't build plots, but build homes for people to rent/buy. Also, keep to the landscape as best you can (if you have to build into a hillside, do it!). I would also design buildings that go well with the mesa (i.e. don't overuse stained clay). Use different color woods, different types of stone, quartz, etc, to contrast the landscape as well as each other. When putting buildings beside each other, don't make everything uniform. 2 buildings that look alike right beside each other, in my mind, is a horrible idea. Also, don't forget to add things for the residents' use, like farms, event areas (PvP, maze, parkour, etc), and social areas. The number one thing for a town to be successful is user friendliness, don't build your town to where the residents are confused, build things simple and at the same time astonishing. That is all I really have to say, any questions feel free to forum pm me, or pm me in game if you see me.