User Interface design is not a pure science, primarily because people's preferences are different. However, there are a few principles that we've learned over the years:
- The eye naturally gravitates to "power points". i.e. in art it is the golden rule, and photography it is simplified to "the rule of thirds". In essence if you drew a grid on your screen three cells across and three cells down, the points where the lines intersect are the power points. These are very important real estate, and it also explains why the 1/3-2/3 split works so well.
- We've learned that there is an order of importance when we learn to read. In short, the most important column on a the screen is the one that comes first in reading order. For us western hemisphere folks, that means the left (left-to-right reading order). For folks in the middle east and some far eastern countries that means the right (right-to-left reading order). For other folks in other far eastern countries that means the top (top-to-bottom, typically right-to-left reading order).
Using these two principles, we can organize the screen in a way that users can get the most out of it. The MS Visual Studio developers surmised that the source code is the most important element, and the other panels support that content.
Now, if you have a preference to have the navigation on the left, it is because you place a different value on the importance of the navigation than the VS developers. Neither position is right or wrong. If you find yourself jumping from file to file often, it can be handy to have the navigation on the left.
You'll notice that even in this site, the content is on the left and the navigation and support information is on the right. This echoes what the designers felt were the most important aspects of the site.