I understand where you're coming from and I am always debating this.
The reason behind Q2A's current design is to allow themes or plugins (via layers) to modify small parts of the page, by overriding the appropriate theme functions. This allows multiple plugins to modify different parts of the page, without interfering with each other. It wouldn't be possible with a template-centered architecture.
On the other hand it makes it harder for non-programmers to make small modifications to the HTML for their pages, and I understand it's a problem.
I think the long term solution is to allow people to choose whether to use templates or not, perhaps on a per-page basis. But this will be a major architectural change and would only appear in a major new version ("Q2A 2.0"?)