A lot of New England towns have local regulations that say that any McDonalds (or other chain business) needs to fit in with the local architectural style. Take a look at the most expensive McDonald's in the country in Lee, MA:

https://maps.app.goo.gl/gWFtn5PRmzHtYq3D9

It's not what you would think a McDonald's looks like; it actually looks basically like every other rest stop on the Mass Pike, which looks like most of the commercial real estate in the area.

There are probably extra costs associated with making the outside of a building look just like every other building, while making the inside conform to McDonald's franchise specifications. Also you lose some of the branding benefit that the nationwide chain has, and the local populace tends to be a bit more hostile toward fast food.