This is a very good point. Sometimes those "quick fixes" really aren't the best idea, I myself used to "hack" so much stuff in Wordpress when I was using it, and yes I solved whatever problem I was having at the time, but a few updates later it would come bite me in the you know what.

So much of programming is protecting the programmer from him or herself. By enforcing rules you protect yourself from bad habits. I think a separate template system and keeping the view separate would help keep everyone honest.

Eventually I started to do my modifications as plugins, which is one area where Wordpress really shines. Other systems could definitely take note of the way WP handles plugins.