wrote:
- is the route box in the flight plan form just an anachronism from
a more flexible time in history

To a certain extent, yes. At least in some parts of the world with
busy airspace, where ATC pretty much just assigns you a canned route.

- why shouldn't I just file DIRECT?

Many people do just that. Personally, I think it's just being lazy.
Look up the routes in the back of the AFD. If your exact
destination/origin isn't there, try and figure out what the most
likely route is based on nearby airports. Or access the FAA route
database on-line (http://tinyurl.com/8w2l). It's always nice to hear
"cleared as filed".

This is all only a minor annoyance, except for when I am sitting in the
runup area with a newly picked up clearance, trying to figure out where
those fixes are while the hobbs meter is running.

See above :-)