I've had cases where the navigable river takes up too many tiles of the capital, and sometimes you get a bad layout of resources or mountains that means it's not as simple to expand to the other side.
But given my capital is generally never going to lose a tile to another settlement, and has the full tile set to work with, even in the worst case if you have a bad river spot, too much water, etc.. maybe I have to skip a warehouse building, or don't have the full free space to get all the wonders in. And when you get later, those nav rivers can make for some juicy markets/inns to help you along too.
For me the "bad" capitals are where you get either a bad resource set, they're too far that you have to build out too much to get to them, or they're just laid out in an annoying way that I have to waste a lot of tiles. Those are the times where I might aim for a restart. But desert is usually good because camels.