In short: I prefer Kenshi but it's due to its genre being my favorite or very-close-second favorite genre of games. But I love and am fascinated by MnB.
To go to unnecessary lengths to clarify:
'Enjoyment' will really depend on who you ask, and when. To me, it depends on what kind of game I want to play at the moment - MnB is a lot more about being in the heat of battle, doing strategy/tactics and keeping your food and money in the green, and beating some silly nobles up.
Kenshi is about surviving every single weird s*** the developers thought would be fun to throw at the players. And its also about doing whatever you want. I don't find much enjoyment in a game like MnB to just hang around a town trying to troll people, meanwhile in Kenshi I could probably lose two hours in each location trying to find weird shit to do while probably dying or getting maimed infinite times in the process.
The only true overlap I can see is that, in both games, the game is not about you. If you want it to be about you, you gotta put in the effort. Otherwise the game and its world has more to do than to care about the player.
In that way, I feel it's also similar to DF and Space Rangers. All those games are included in my favorite games list..but I wouldn't be able to say which one I enjoy more.
DF of course praise ARMOK long live THE TOAD the only reason I don't play DF more is because I fear forgetting about REAL LIFE They are all different, and what I feel like playing is also different every few days.
Some critical differences that makes me choose between one or the other comes from MnB abstracting a lot of stuff into text screens or simply teleporting/fast-forwarding, whereas everything actually happen in real-time in Kenshi. Camping, eating, getting tortured, being a slave, etc. This is done because it's not the focus of the MnB and all that. And in MnB you directly control your character, of course.
MnB characters in your parties also have their personalities and values, something that (at least in my experience) don't really happen in Kenshi . It's all up to you to roleplay. Even though unique companions may have unique lines they utter when going into certain places, every character can and is pretty much a bot once you assign jobs to them. It's very cool to be able to go out with your "exploration squad" and leave your 'civilians' automatically taking care of your town, but if you're into DF-style / colony sim games, eventually it feels a little void and sad since they don't have any needs, personalities or socialization. At least after they got the need for food, it doesn't 100% feel like they are just robots. Then again, in MnB you also don't get to see them interacting with each other, going to eat or etc, but since the game 'fast-forwards' during camping, town visits and so on, your mind probably fills that gap consciously (roleplay) or uncounsciouly.
Anyways, to me it boils down on whether I want to get personal (as mentioned by Micro102 above), macro and abstract, or impersonal, micro-y and specific.