Spoken like a true hacker.
Too often a site discussed on HN is criticized for a design decision that is easily changeable on the client. Anything that is slightly inconvenient for one specific workflow is a "misfeature", ignoring entirely that many people like it that way. A site designer cannot please everyone.
Most non-hackers do not even notice this stuff. Go find a normal person and ask them to list the sites they visit and whether or not they auto-focus the search box. They do not notice. We are the weird ones.
If it annoys you, change it. You have the power. Most of the time what you want can be accomplished with a simple extension, no coding required.
If not, you can write your own extension, or write a script for an extension, or "use" browsers like uzbl and luakit, or write your own browser. Then you can put your solution on the web, so other people can benefit.