The spaces are linear instead of in a grid because now we can swipe to move between spaces - a huge advantage and time saver and worth every "inconvenience" you've described. And in Mission Control it's very easy to reorder the spaces, just grab one with the mouse and move it.
You could still swipe if it was a grid. It would actually be easier than linear.
You couldn't move spaces when lion first came out, which is when this was written. But try moving windows from space to space. Way worse.
I, and just about everyone else who has responded to this post, completely disagrees with your ridiculous statement that spaces now only working in one dimension is better and worth the many many other "inconveniences."