The problem with not filing a fix every couple hundred miles is that it sometimes causes problems with the flight plan processing. In simple terms, the ATC computers need to be able to accurately project you flight path so your Flight Plan info, (strips) go to the correct sector, and so the automated handoff functions correctly. (Hands off to the correct sector).
If you're using GPS, the fix need not be a VOR, but those are best. You can use an airfield identifier or published intersection. It's really not normally that hard to pick a fix of some sort every couple hundred miles to define your desired route. The fact that you might make a 5 degree dog-leg in the middle of a 400 mile trip isn't going to add diddly to your ETA or fuel burn.
Departing and Arriving, the NAS will most often assign a DP and/or STAR, if appropriate, whether you file it or not, and the controller will simply issue that. Problems occur when we have to keep amending the route to get the NAS to process the clearance properly and update the progress of the flight. I hate having to take my eyes off of the scope to go "fix" a flight plan when it's busy, and all controllers hate verbal coordination with another facility when it's busy. It can get darn near impossible to find 20 seconds when one or the other of us isn't busy talking to aircraft. This leads to having to repeat ourselves several times, and causes us to have to then "catch up" on our next dozen tasks.
This is less of a problem in the high, enroute sectors, where sector boundries may be 100 miles or more apart. When you get down to below 14,000 though, sector or airspace boundries may only be 20-30 miles apart. Every sector needs a strip and a handoff or point out.
It really doesn't bug me that pilots don't know the correct DP or STAR to file. How would they unless the FAA had better publications? I just appreciate those that make the effort. When I get one that files diredt to destination 400 or more miles away though, without even an effort to define a route, then lets just say I don't feel too bad about the NAS routing them via victor airways for the first 100 or so miles. I realize that someone other than the crew files many flight plans for the fractionals and larger corporate operators, and perhaps some of the Web based FP services are also part of the problem.
I do offer and generate a lot of "shortcuts", asked for or not, when I have time for such. But there are times I just can't stop vectoring long enough to fix a lousy routing. Having help at the position works, but there normally isn't any unless a Supe helps out. We don't have enuf controller bodies anymore to staff a Handoff or "helper" position.