It's on the left in both of my towns. I have visited a lot of other towns, but I rarely go up to Main Street to shop or visit the museum when I'm visiting. I didn't realize the layout could be different!
The museum in my main town is on the left and one of my other towns has it on the right. Because I was so used to the main town and having it on the left for a long time, when I found the other one had it on the right it kinda messed with my head. It just looks better on the left, in my opinion.
2 of my towns have it on the right and one has it on the left. Having it on the left side is really annoying imo cuz I never go that far in on that side of main street.
Mine was originally on the right side for the first two towns I made in my copy. My current town however, has the museum located on the left and it is still pretty jarring for me! Like dinomates, I also don't usually go that far down the left side of main street, but I'm starting to grow used to it. When the museums are set up on the left, it leave only shops on the right, which is better organized in my opinion.