What are all the differences between Minutemen versus Brotherhood of Steel being in control of a location?

Only some of the settlements (Roughly just over half) can be turned into allies of the Brotherhood of Steel. These select settlements can also be turned into safe houses for the railroad if they aren't already allied with the minutemen or BOS.

In terms of gameplay the Brotherhood had better weapons and equipment than the minutemen. If you haven't destroyed the Prydwen, you are far more likely to encounter a BOS patrol in the commonwealth than a Minutemen one, meaning that if your settlement is attacked you have a small chance to encounter a patrol to help you out.

You may wonder about artillery support. It may be a bug but I am able to build artillery in any of my settlements no matter what affiliation. So long as you've done the castle quest you can build them.

Ultimately they are similar enough that it's a role-playing choice for each location.